rs909475

Variant names:

• chr6-170504701-T-C
• rs909475
• ENST00000722532.1:n.122-16195A>G

Variant summary

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

The ENST00000722532.1(ENSG00000294293):​n.122-16195A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000294293 ENST00000722532.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.315
• Publications: 6 publications found

Genes affected

ENSG00000294293 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000294293	ENST00000722532.1	n.122-16195A>G		intron_variant	Intron 1 of 3

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

African (AFR) AF: 0.800 AC: 33208 AN: 41488

American (AMR) AF: 0.652 AC: 9974 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.713 AC: 2474 AN: 3472

East Asian (EAS) AF: 0.294 AC: 1519 AN: 5170

South Asian (SAS) AF: 0.609 AC: 2933 AN: 4818

European-Finnish (FIN) AF: 0.572 AC: 6044 AN: 10560

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.601 AC: 40842 AN: 67966

Other (OTH) AF: 0.637 AC: 1347 AN: 2114

Alfa AF: 0.625 Hom.: 13853

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
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs909475; hg19: chr6-170813789;