rs9471535

Variant names:

• chr6-41287752-T-C
• rs9471535

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.119 in 152,200 control chromosomes in the GnomAD database, including 1,214 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 0.12 (1214 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.546
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.293 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: 0.119 AC: 18101 AN: 152084 Hom.: 1207 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.0954

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.119 AC: 18125 AN: 152200 Hom.: 1214 Cov.: 32 AF XY: 0.122 AC XY: 9056 AN XY: 74404

African (AFR) AF: 0.131 AC: 5431 AN: 41530

American (AMR) AF: 0.126 AC: 1924 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 367 AN: 3470

East Asian (EAS) AF: 0.306 AC: 1584 AN: 5176

South Asian (SAS) AF: 0.130 AC: 629 AN: 4820

European-Finnish (FIN) AF: 0.122 AC: 1287 AN: 10568

Middle Eastern (MID) AF: 0.0925 AC: 27 AN: 292

European-Non Finnish (NFE) AF: 0.0954 AC: 6493 AN: 68026

Other (OTH) AF: 0.126 AC: 266 AN: 2104

Alfa AF: 0.118 Hom.: 130

Bravo AF: 0.122

Asia WGS AF: 0.216 AC: 749 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.4
DANN	Benign	0.82
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs9471535; hg19: chr6-41255490;