rs7671659

Variant names:

• chr4-34351926-G-A
• rs7671659

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 0.334 in 151,938 control chromosomes in the GnomAD database, including 12,840 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 0.33 (12840 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.965
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.706 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: 0.333 AC: 50612 AN: 151818 Hom.: 12790 Cov.: 32

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.334 AC: 50726 AN: 151938 Hom.: 12840 Cov.: 32 AF XY: 0.333 AC XY: 24740 AN XY: 74246

African (AFR) AF: 0.713 AC: 29554 AN: 41436

American (AMR) AF: 0.255 AC: 3892 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 769 AN: 3468

East Asian (EAS) AF: 0.134 AC: 690 AN: 5152

South Asian (SAS) AF: 0.353 AC: 1698 AN: 4804

European-Finnish (FIN) AF: 0.189 AC: 1992 AN: 10544

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11397 AN: 67950

Other (OTH) AF: 0.291 AC: 613 AN: 2104

Alfa AF: 0.242 Hom.: 3197

Bravo AF: 0.351

Asia WGS AF: 0.315 AC: 1096 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.061
DANN	Benign	0.18
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs7671659; hg19: chr4-34353548;