rs7659604

Variant names:

• chr4-121744359-C-T
• rs7659604

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 0.481 in 152,022 control chromosomes in the GnomAD database, including 18,769 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 0.48 (18769 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347
• Publications: 42 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.664 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: 0.481 AC: 73012 AN: 151902 Hom.: 18750 Cov.: 32

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.481 AC: 73070 AN: 152022 Hom.: 18769 Cov.: 32 AF XY: 0.478 AC XY: 35536 AN XY: 74280

African (AFR) AF: 0.670 AC: 27793 AN: 41464

American (AMR) AF: 0.340 AC: 5193 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1504 AN: 3472

East Asian (EAS) AF: 0.379 AC: 1962 AN: 5174

South Asian (SAS) AF: 0.459 AC: 2208 AN: 4814

European-Finnish (FIN) AF: 0.455 AC: 4794 AN: 10546

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.415 AC: 28221 AN: 67960

Other (OTH) AF: 0.474 AC: 1003 AN: 2114

Alfa AF: 0.446 Hom.: 24598

Bravo AF: 0.476

Asia WGS AF: 0.431 AC: 1497 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.27
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs7659604; hg19: chr4-122665514;