rs9564944

Variant names:

• chr13-73086844-G-A
• rs9564944

Your query was ambiguous. Multiple possible variants found:

• chr13-73086844-G-A
• chr13-73086844-G-C
• chr13-73086844-G-T

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 0.128 in 152,124 control chromosomes in the GnomAD database, including 2,032 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 0.13 (2032 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.491 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: 0.128 AC: 19385 AN: 152006 Hom.: 2024 Cov.: 32

Gnomad AFR AF: 0.0451

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.0885

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.128 AC: 19402 AN: 152124 Hom.: 2032 Cov.: 32 AF XY: 0.136 AC XY: 10100 AN XY: 74378

African (AFR) AF: 0.0450 AC: 1871 AN: 41538

American (AMR) AF: 0.244 AC: 3723 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0885 AC: 307 AN: 3470

East Asian (EAS) AF: 0.507 AC: 2612 AN: 5154

South Asian (SAS) AF: 0.257 AC: 1240 AN: 4820

European-Finnish (FIN) AF: 0.146 AC: 1547 AN: 10576

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7743 AN: 67992

Other (OTH) AF: 0.135 AC: 285 AN: 2112

Alfa AF: 0.123 Hom.: 2798

Bravo AF: 0.133

Asia WGS AF: 0.363 AC: 1262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.3
DANN	Benign	0.73
PhyloP100		0.078

Splicing

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

Other links and lift over

dbSNP: rs9564944; hg19: chr13-73660982;