4-17437723-A-G

Variant names:

• chr4-17437723-A-G
• rs7671329

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 0.427 in 152,014 control chromosomes in the GnomAD database, including 14,387 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 0.43 (14387 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64834 AN: 151896 Hom.: 14385 Cov.: 32

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.427 AC: 64860 AN: 152014 Hom.: 14387 Cov.: 32 AF XY: 0.421 AC XY: 31262 AN XY: 74312

African (AFR) AF: 0.420 AC: 17400 AN: 41452

American (AMR) AF: 0.335 AC: 5115 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1279 AN: 3468

East Asian (EAS) AF: 0.104 AC: 539 AN: 5166

South Asian (SAS) AF: 0.342 AC: 1650 AN: 4826

European-Finnish (FIN) AF: 0.443 AC: 4689 AN: 10574

Middle Eastern (MID) AF: 0.377 AC: 110 AN: 292

European-Non Finnish (NFE) AF: 0.481 AC: 32703 AN: 67936

Other (OTH) AF: 0.431 AC: 912 AN: 2114

Alfa AF: 0.457 Hom.: 62461

Bravo AF: 0.419

Asia WGS AF: 0.256 AC: 891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.4
DANN	Benign	0.76
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs7671329; hg19: chr4-17439346;