rs7356274

Variant names:

• chr4-124920932-A-G
• rs7356274

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 0.0664 in 152,074 control chromosomes in the GnomAD database, including 377 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 0.066 (377 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.424
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.102 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: 0.0663 AC: 10082 AN: 151956 Hom.: 373 Cov.: 33

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.0489

Gnomad ASJ AF: 0.0618

Gnomad EAS AF: 0.0133

Gnomad SAS AF: 0.0751

Gnomad FIN AF: 0.0577

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0512

Gnomad OTH AF: 0.0656

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

GnomAD4 genome AF: 0.0664 AC: 10100 AN: 152074 Hom.: 377 Cov.: 33 AF XY: 0.0655 AC XY: 4867 AN XY: 74352

African (AFR) AF: 0.105 AC: 4341 AN: 41476

American (AMR) AF: 0.0488 AC: 745 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0618 AC: 214 AN: 3464

East Asian (EAS) AF: 0.0133 AC: 69 AN: 5180

South Asian (SAS) AF: 0.0760 AC: 367 AN: 4830

European-Finnish (FIN) AF: 0.0577 AC: 612 AN: 10602

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0511 AC: 3473 AN: 67924

Other (OTH) AF: 0.0644 AC: 136 AN: 2112

Alfa AF: 0.0566 Hom.: 125

Bravo AF: 0.0675

Asia WGS AF: 0.0400 AC: 137 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.80
DANN	Benign	0.60
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs7356274; hg19: chr4-125842087;