rs9390537

Variant names:

• chr6-148102235-C-T
• rs9390537

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 0.724 in 151,828 control chromosomes in the GnomAD database, including 40,804 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 0.72 (40804 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.793 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: 0.724 AC: 109827 AN: 151712 Hom.: 40785 Cov.: 29

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.798

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.799

Gnomad OTH AF: 0.727

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

GnomAD4 genome AF: 0.724 AC: 109886 AN: 151828 Hom.: 40804 Cov.: 29 AF XY: 0.713 AC XY: 52935 AN XY: 74194

Gnomad4 AFR AF: 0.708

Gnomad4 AMR AF: 0.567

Gnomad4 ASJ AF: 0.733

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.520

Gnomad4 FIN AF: 0.798

Gnomad4 NFE AF: 0.799

Gnomad4 OTH AF: 0.720

Alfa AF: 0.759 Hom.: 44320

Bravo AF: 0.704

Asia WGS AF: 0.403 AC: 1407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.9
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9390537; hg19: chr6-148423371;