rs9317975

Variant names:

• chr13-70932106-G-A
• rs9317975

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 0.347 in 151,708 control chromosomes in the GnomAD database, including 9,456 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 0.35 (9456 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.17
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52593 AN: 151588 Hom.: 9444 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.347 AC: 52632 AN: 151708 Hom.: 9456 Cov.: 32 AF XY: 0.350 AC XY: 25969 AN XY: 74106

African (AFR) AF: 0.262 AC: 10831 AN: 41402

American (AMR) AF: 0.408 AC: 6218 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1458 AN: 3464

East Asian (EAS) AF: 0.292 AC: 1504 AN: 5158

South Asian (SAS) AF: 0.335 AC: 1618 AN: 4824

European-Finnish (FIN) AF: 0.463 AC: 4849 AN: 10474

Middle Eastern (MID) AF: 0.367 AC: 105 AN: 286

European-Non Finnish (NFE) AF: 0.371 AC: 25171 AN: 67856

Other (OTH) AF: 0.350 AC: 735 AN: 2100

Alfa AF: 0.365 Hom.: 1322

Bravo AF: 0.340

Asia WGS AF: 0.283 AC: 983 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	8.3
DANN	Benign	0.36
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs9317975; hg19: chr13-71506238;