3-39199946-T-C

Variant names:

• chr3-39199946-T-C
• rs4676483
• ENST00000720013.1:n.195+7514T>C

Variant summary

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

The ENST00000720013.1(ENSG00000287620):​n.195+7514T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.735 in 152,274 control chromosomes in the GnomAD database, including 43,613 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 0.74 (43613 hom., cov: 34)
• Consequence: ENSG00000287620 ENST00000720013.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0560
• Publications: 7 publications found

Genes affected

ENSG00000287620 (HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287620	ENST00000720013.1	n.195+7514T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.735 AC: 111885 AN: 152156 Hom.: 43590 Cov.: 34

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.794

Gnomad SAS AF: 0.894

Gnomad FIN AF: 0.936

Gnomad MID AF: 0.787

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.735 AC: 111957 AN: 152274 Hom.: 43613 Cov.: 34 AF XY: 0.743 AC XY: 55353 AN XY: 74460

African (AFR) AF: 0.457 AC: 18996 AN: 41528

American (AMR) AF: 0.764 AC: 11692 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.842 AC: 2925 AN: 3472

East Asian (EAS) AF: 0.794 AC: 4117 AN: 5188

South Asian (SAS) AF: 0.893 AC: 4312 AN: 4830

European-Finnish (FIN) AF: 0.936 AC: 9944 AN: 10620

Middle Eastern (MID) AF: 0.777 AC: 227 AN: 292

European-Non Finnish (NFE) AF: 0.843 AC: 57371 AN: 68016

Other (OTH) AF: 0.743 AC: 1571 AN: 2114

Alfa AF: 0.812 Hom.: 85465

Bravo AF: 0.705

Asia WGS AF: 0.841 AC: 2924 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.1
DANN	Benign	0.45
PhyloP100		0.056

Splicing

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

Other links and lift over

dbSNP: rs4676483; hg19: chr3-39241437;