rs7356274

chr4-124920932-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.0488

Gnomad4 ASJ AF: 0.0618

Gnomad4 EAS AF: 0.0133

Gnomad4 SAS AF: 0.0760

Gnomad4 FIN AF: 0.0577

Gnomad4 NFE AF: 0.0511

Gnomad4 OTH AF: 0.0644

Alfa AF: 0.0564 Hom.: 108

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7356274; hg19: chr4-125842087;