rs4256662

Positions:

• chr9-37038261-G-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;