rs369397772

Variant names:

• chr15-40458921-C-A
• NM_014952.5:c.457C>A

Your query was ambiguous. Multiple possible variants found:

• chr15-40458921-C-A
• chr15-40458921-C-G
• chr15-40458921-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_014952.5(BAHD1):​c.457C>A​(p.Arg153Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000138 in 1,444,584 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict 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. R153C) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: BAHD1 NM_014952.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.865

Genes affected

BAHD1 (HGNC:29153): (bromo adjacent homology domain containing 1) Enables chromatin binding activity. Involved in heterochromatin assembly and negative regulation of transcription, DNA-templated. Located in nucleoplasm. Part of chromatin silencing complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.090873).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BAHD1	NM_014952.5	c.457C>A	p.Arg153Ser	missense_variant	Exon 2 of 7	ENST00000416165.6	NP_055767.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BAHD1	ENST00000416165.6	c.457C>A	p.Arg153Ser	missense_variant	Exon 2 of 7	1	NM_014952.5	ENSP00000396976.1
BAHD1	ENST00000561234.5	c.457C>A	p.Arg153Ser	missense_variant	Exon 2 of 7	1		ENSP00000454150.1
BAHD1	ENST00000560846.1	c.457C>A	p.Arg153Ser	missense_variant	Exon 1 of 6	1		ENSP00000454101.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000138 AC: 2 AN: 1444584 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 716774

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000181

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.16
BayesDel_addAF	Benign	-0.051	T
BayesDel_noAF	Benign	-0.31
CADD	Benign	16
DANN	Benign	0.96
DEOGEN2	Benign	0.038	.;T;.
Eigen	Benign	-0.84
Eigen_PC	Benign	-0.71
FATHMM_MKL	Benign	0.27	N
LIST_S2	Benign	0.75	T;T;T
M_CAP	Benign	0.011	T
MetaRNN	Benign	0.091	T;T;T
MetaSVM	Benign	-0.97	T
MutationAssessor	Benign	0.55	N;N;N
PrimateAI	Uncertain	0.49	T
PROVEAN	Benign	0.75	N;N;N
REVEL	Benign	0.23
Sift	Benign	0.057	T;T;D
Sift4G	Benign	0.77	T;T;T
Polyphen		0.081	B;B;B
Vest4		0.33
MutPred		0.23		Gain of phosphorylation at R153 (P = 0.0033);Gain of phosphorylation at R153 (P = 0.0033);Gain of phosphorylation at R153 (P = 0.0033);
MVP		0.77
MPC		0.28
ClinPred		0.16	T
GERP RS		3.5
Varity_R		0.11
gMVP		0.23

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr15-40751120;