rs9501958

chr6-378970-G-A

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 0.0927 in 148,122 control chromosomes in the GnomAD database, including 27 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 0.093 (27 hom., cov: 59)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.105

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.192 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: 0.0925 AC: 13696 AN: 148022 Hom.: 27 Cov.: 59

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.0770

Gnomad ASJ AF: 0.0589

Gnomad EAS AF: 0.0198

Gnomad SAS AF: 0.0403

Gnomad FIN AF: 0.0380

Gnomad MID AF: 0.119

Gnomad NFE AF: 0.0543

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.0927 AC: 13729 AN: 148122 Hom.: 27 Cov.: 59 AF XY: 0.0910 AC XY: 6591 AN XY: 72454

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.0768

Gnomad4 ASJ AF: 0.0589

Gnomad4 EAS AF: 0.0199

Gnomad4 SAS AF: 0.0401

Gnomad4 FIN AF: 0.0380

Gnomad4 NFE AF: 0.0543

Gnomad4 OTH AF: 0.102

Alfa AF: 0.0687 Hom.: 59

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	2.5
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9501958; hg19: chr6-378970;