12-26122364-G-T

Variant names:

• chr12-26122364-G-T
• rs121912617
• NM_030762.3:c.1151C>A

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_030762.3(BHLHE41):​c.1151C>A​(p.Pro384Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000839 in 1,180,614 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P384R) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.0045 (5 hom., cov: 30)
  • Exomes 𝑓: 0.00031 (1 hom.)
• Consequence: BHLHE41 NM_030762.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 8.21
• Publications: 15 publications found

Genes affected

BHLHE41 (HGNC:16617): (basic helix-loop-helix family member e41) This gene encodes a basic helix-loop-helix protein expressed in various tissues. The encoded protein can interact with ARNTL or compete for E-box binding sites in the promoter of PER1 and repress CLOCK/ARNTL's transactivation of PER1. This gene is believed to be involved in the control of circadian rhythm and cell differentiation. Defects in this gene are associated with the short sleep phenotype. [provided by RefSeq, Feb 2014]

SSPN (HGNC:11322): (sarcospan) This gene encodes a member of the dystrophin-glycoprotein complex (DGC). The DGC spans the sarcolemma and is comprised of dystrophin, syntrophin, alpha- and beta-dystroglycans and sarcoglycans. The DGC provides a structural link between the subsarcolemmal cytoskeleton and the extracellular matrix of muscle cells. Two alternatively spliced transcript variants that encode different protein isoforms have been described. [provided by RefSeq, Oct 2008]

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.006427467).
• BS2: High AC in GnomAd4 at 666 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030762.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BHLHE41	NM_030762.3	MANE Select	c.1151C>A	p.Pro384Gln	missense	Exon 5 of 5	NP_110389.1	Q9C0J9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BHLHE41	ENST00000242728.5	TSL:1 MANE Select	c.1151C>A	p.Pro384Gln	missense	Exon 5 of 5	ENSP00000242728.4	Q9C0J9
	BHLHE41	ENST00000957109.1		c.1157C>A	p.Pro386Gln	missense	Exon 5 of 5	ENSP00000627168.1
	SSPN	ENST00000538142.5	TSL:4	c.-31+212G>T		intron	N/A	ENSP00000445360.1	F5H381

Frequencies

GnomAD3 genomes AF: 0.00451 AC: 666 AN: 147600 Hom.: 5 Cov.: 30

Gnomad AFR AF: 0.0138

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00583

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000453

Gnomad OTH AF: 0.00586

GnomAD2 exomes AF: 0.000182 AC: 2 AN: 10992 AF XY: 0.00

Gnomad AFR exome AF: 0.00725

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.000314 AC: 324 AN: 1032898 Hom.: 1 Cov.: 30 AF XY: 0.000316 AC XY: 155 AN XY: 490622

African (AFR) AF: 0.0115 AC: 238 AN: 20728

American (AMR) AF: 0.00215 AC: 16 AN: 7456

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11842

East Asian (EAS) AF: 0.00 AC: 0 AN: 21140

South Asian (SAS) AF: 0.00 AC: 0 AN: 20982

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 20688

Middle Eastern (MID) AF: 0.000363 AC: 1 AN: 2758

European-Non Finnish (NFE) AF: 0.0000327 AC: 29 AN: 888008

Other (OTH) AF: 0.00102 AC: 40 AN: 39296

GnomAD4 genome AF: 0.00451 AC: 666 AN: 147716 Hom.: 5 Cov.: 30 AF XY: 0.00407 AC XY: 293 AN XY: 72008

African (AFR) AF: 0.0138 AC: 564 AN: 40900

American (AMR) AF: 0.00582 AC: 87 AN: 14946

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3408

East Asian (EAS) AF: 0.00 AC: 0 AN: 4914

South Asian (SAS) AF: 0.00 AC: 0 AN: 4728

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9284

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.0000453 AC: 3 AN: 66268

Other (OTH) AF: 0.00580 AC: 12 AN: 2070

Alfa AF: 0.00474 Hom.: 0

ExAC AF: 0.000285 AC: 27

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.32
BayesDel_addAF	Benign	-0.24	T
BayesDel_noAF	Benign	-0.11
CADD	Benign	23
DANN	Uncertain	0.98
DEOGEN2	Benign	0.17	T
Eigen	Benign	0.19
Eigen_PC	Benign	0.13
FATHMM_MKL	Uncertain	0.93	D
LIST_S2	Benign	0.78	T
MetaRNN	Benign	0.0064	T
MetaSVM	Benign	-0.54	T
MutationAssessor	Benign	0.81	L
PhyloP100		8.2
PrimateAI	Pathogenic	0.89	D
PROVEAN	Benign	-2.0	N
REVEL	Uncertain	0.57
Sift	Uncertain	0.0020	D
Sift4G	Uncertain	0.010	D
Polyphen		0.96	D
Vest4		0.40
MVP		0.52
ClinPred		0.21	T
GERP RS		3.1
PromoterAI		0.023	Neutral
Varity_R		0.15
gMVP		0.67
Mutation Taster		=78/22	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs121912617; hg19: chr12-26275297;