rs909475

Variant names:

• chr6-170504701-T-C
• rs909475

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 0.65 in 152,090 control chromosomes in the GnomAD database, including 33,159 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 0.65 (33159 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.315

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 = 0.793 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: 0.650 AC: 98807 AN: 151972 Hom.: 33113 Cov.: 32

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.641

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

GnomAD4 genome AF: 0.650 AC: 98908 AN: 152090 Hom.: 33159 Cov.: 32 AF XY: 0.647 AC XY: 48098 AN XY: 74334

Gnomad4 AFR AF: 0.800

Gnomad4 AMR AF: 0.652

Gnomad4 ASJ AF: 0.713

Gnomad4 EAS AF: 0.294

Gnomad4 SAS AF: 0.609

Gnomad4 FIN AF: 0.572

Gnomad4 NFE AF: 0.601

Gnomad4 OTH AF: 0.637

Alfa AF: 0.622 Hom.: 7995

Bravo AF: 0.654

Asia WGS AF: 0.485 AC: 1689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.9
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs909475; hg19: chr6-170813789;