rs4256662

Variant names:

• chr9-37038261-G-T
• rs4256662

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 0.761 in 152,288 control chromosomes in the GnomAD database, including 47,604 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 0.76 (47604 hom., cov: 36)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.969

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.909 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: 0.761 AC: 115793 AN: 152170 Hom.: 47586 Cov.: 36

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.945

Gnomad AMR AF: 0.836

Gnomad ASJ AF: 0.893

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.909

Gnomad FIN AF: 0.897

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.915

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.761 AC: 115835 AN: 152288 Hom.: 47604 Cov.: 36 AF XY: 0.764 AC XY: 56924 AN XY: 74484

Gnomad4 AFR AF: 0.416

Gnomad4 AMR AF: 0.836

Gnomad4 ASJ AF: 0.893

Gnomad4 EAS AF: 0.704

Gnomad4 SAS AF: 0.909

Gnomad4 FIN AF: 0.897

Gnomad4 NFE AF: 0.915

Gnomad4 OTH AF: 0.800

Alfa AF: 0.889 Hom.: 69166

Bravo AF: 0.737

Asia WGS AF: 0.796 AC: 2769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.36
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4256662; hg19: chr9-37038258;