rs7657504

Variant names:

• chr4-69565871-G-A
• rs7657504

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 0.353 in 151,686 control chromosomes in the GnomAD database, including 9,539 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 0.35 (9539 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.271
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.372 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: 0.353 AC: 53558 AN: 151566 Hom.: 9536 Cov.: 31

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.353 AC: 53595 AN: 151686 Hom.: 9539 Cov.: 31 AF XY: 0.348 AC XY: 25770 AN XY: 74118

African (AFR) AF: 0.352 AC: 14581 AN: 41382

American (AMR) AF: 0.319 AC: 4852 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1223 AN: 3468

East Asian (EAS) AF: 0.251 AC: 1293 AN: 5146

South Asian (SAS) AF: 0.342 AC: 1646 AN: 4806

European-Finnish (FIN) AF: 0.320 AC: 3362 AN: 10512

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.376 AC: 25487 AN: 67842

Other (OTH) AF: 0.355 AC: 747 AN: 2106

Alfa AF: 0.366 Hom.: 1748

Bravo AF: 0.353

Asia WGS AF: 0.299 AC: 1038 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.58
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs7657504; hg19: chr4-70431589;