chr4-171437593-T-G

Variant names:

• chr4-171437593-T-G
• rs3907555

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 0.644 in 151,672 control chromosomes in the GnomAD database, including 32,643 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 0.64 (32643 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97595 AN: 151554 Hom.: 32633 Cov.: 32

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.801

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.644 AC: 97646 AN: 151672 Hom.: 32643 Cov.: 32 AF XY: 0.651 AC XY: 48250 AN XY: 74116

African (AFR) AF: 0.448 AC: 18566 AN: 41426

American (AMR) AF: 0.732 AC: 11131 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.666 AC: 2303 AN: 3456

East Asian (EAS) AF: 0.801 AC: 4145 AN: 5172

South Asian (SAS) AF: 0.652 AC: 3146 AN: 4824

European-Finnish (FIN) AF: 0.780 AC: 8247 AN: 10572

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.710 AC: 48052 AN: 67708

Other (OTH) AF: 0.636 AC: 1340 AN: 2108

Alfa AF: 0.683 Hom.: 4528

Bravo AF: 0.630

Asia WGS AF: 0.751 AC: 2605 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4
DANN	Benign	0.58
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs3907555; hg19: chr4-172358744;