3-39541433-C-T

Variant names:

• chr3-39541433-C-T
• rs1606473

Variant summary

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

The variant allele was found at a frequency of 0.613 in 151,952 control chromosomes in the GnomAD database, including 32,365 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 0.61 (32365 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.881
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.765 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

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93117 AN: 151836 Hom.: 32369 Cov.: 31

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.722

Gnomad EAS AF: 0.623

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.787

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.613 AC: 93112 AN: 151952 Hom.: 32365 Cov.: 31 AF XY: 0.616 AC XY: 45753 AN XY: 74270

African (AFR) AF: 0.259 AC: 10720 AN: 41376

American (AMR) AF: 0.679 AC: 10356 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.722 AC: 2503 AN: 3468

East Asian (EAS) AF: 0.622 AC: 3214 AN: 5164

South Asian (SAS) AF: 0.684 AC: 3290 AN: 4812

European-Finnish (FIN) AF: 0.787 AC: 8320 AN: 10574

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.770 AC: 52365 AN: 67994

Other (OTH) AF: 0.631 AC: 1329 AN: 2106

Alfa AF: 0.733 Hom.: 24596

Bravo AF: 0.588

Asia WGS AF: 0.611 AC: 2126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.44
DANN	Benign	0.58
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs1606473; hg19: chr3-39582924;