rs9564447

Variant names:

• chr13-68326220-G-A
• rs9564447

Your query was ambiguous. Multiple possible variants found:

• chr13-68326220-G-A
• chr13-68326220-G-C

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 0.537 in 151,914 control chromosomes in the GnomAD database, including 23,324 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 0.54 (23324 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.281
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.63 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: 0.537 AC: 81544 AN: 151796 Hom.: 23314 Cov.: 33

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.537 AC: 81567 AN: 151914 Hom.: 23324 Cov.: 33 AF XY: 0.537 AC XY: 39855 AN XY: 74250

African (AFR) AF: 0.329 AC: 13632 AN: 41382

American (AMR) AF: 0.641 AC: 9776 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2054 AN: 3472

East Asian (EAS) AF: 0.512 AC: 2650 AN: 5172

South Asian (SAS) AF: 0.582 AC: 2807 AN: 4822

European-Finnish (FIN) AF: 0.569 AC: 6000 AN: 10536

Middle Eastern (MID) AF: 0.527 AC: 154 AN: 292

European-Non Finnish (NFE) AF: 0.629 AC: 42770 AN: 67958

Other (OTH) AF: 0.564 AC: 1188 AN: 2108

Alfa AF: 0.609 Hom.: 15886

Bravo AF: 0.532

Asia WGS AF: 0.511 AC: 1769 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.3
DANN	Benign	0.69
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs9564447; hg19: chr13-68900352;