chr4-86877043-A-G

Variant names:

• chr4-86877043-A-G
• rs1374934
• NM_144645.4:c.*3-600T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_144645.4(C4orf36):​c.*3-600T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.915 in 152,234 control chromosomes in the GnomAD database, including 64,672 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.

• Frequency: Genomes: 𝑓 0.91 (64672 hom., cov: 33)
• Consequence: C4orf36 NM_144645.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260
• Publications: 3 publications found

Genes affected

C4orf36 (HGNC:28386): (chromosome 4 open reading frame 36)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.989 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_144645.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C4orf36	NM_144645.4	MANE Select	c.*3-600T>C		intron	N/A	NP_653246.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C4orf36	ENST00000295898.8	TSL:1 MANE Select	c.*3-600T>C		intron	N/A	ENSP00000295898.3

Frequencies

GnomAD3 genomes AF: 0.915 AC: 139153 AN: 152116 Hom.: 64640 Cov.: 33

Gnomad AFR AF: 0.735

Gnomad AMI AF: 0.995

Gnomad AMR AF: 0.958

Gnomad ASJ AF: 0.961

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.935

Gnomad FIN AF: 0.999

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.995

Gnomad OTH AF: 0.925

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.915 AC: 139237 AN: 152234 Hom.: 64672 Cov.: 33 AF XY: 0.915 AC XY: 68115 AN XY: 74452

African (AFR) AF: 0.735 AC: 30462 AN: 41470

American (AMR) AF: 0.958 AC: 14653 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.961 AC: 3335 AN: 3472

East Asian (EAS) AF: 0.930 AC: 4823 AN: 5186

South Asian (SAS) AF: 0.935 AC: 4520 AN: 4832

European-Finnish (FIN) AF: 0.999 AC: 10607 AN: 10616

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.995 AC: 67705 AN: 68044

Other (OTH) AF: 0.926 AC: 1955 AN: 2112

Alfa AF: 0.962 Hom.: 177839

Bravo AF: 0.904

Asia WGS AF: 0.926 AC: 3216 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	6.4
DANN	Benign	0.44
PhyloP100		0.026
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1374934; hg19: chr4-87798196;