rs7671764

Variant names:

• chr4-129473649-T-C
• rs7671764

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 0.292 in 152,000 control chromosomes in the GnomAD database, including 6,785 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 0.29 (6785 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.295
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.354 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: 0.292 AC: 44334 AN: 151882 Hom.: 6781 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.292 AC: 44368 AN: 152000 Hom.: 6785 Cov.: 32 AF XY: 0.293 AC XY: 21775 AN XY: 74302

African (AFR) AF: 0.359 AC: 14864 AN: 41458

American (AMR) AF: 0.246 AC: 3761 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1148 AN: 3464

East Asian (EAS) AF: 0.323 AC: 1663 AN: 5152

South Asian (SAS) AF: 0.310 AC: 1495 AN: 4826

European-Finnish (FIN) AF: 0.293 AC: 3098 AN: 10586

Middle Eastern (MID) AF: 0.277 AC: 81 AN: 292

European-Non Finnish (NFE) AF: 0.257 AC: 17480 AN: 67922

Other (OTH) AF: 0.297 AC: 628 AN: 2112

Alfa AF: 0.275 Hom.: 3483

Bravo AF: 0.295

Asia WGS AF: 0.281 AC: 975 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.0
DANN	Benign	0.47
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs7671764; hg19: chr4-130394804;