13-69008553-T-A

Variant names:

• chr13-69008553-T-A
• rs9317760

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 0.555 in 151,932 control chromosomes in the GnomAD database, including 23,662 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 0.56 (23662 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84335 AN: 151814 Hom.: 23644 Cov.: 32

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.555 AC: 84395 AN: 151932 Hom.: 23662 Cov.: 32 AF XY: 0.553 AC XY: 41085 AN XY: 74250

African (AFR) AF: 0.559 AC: 23175 AN: 41454

American (AMR) AF: 0.513 AC: 7829 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2089 AN: 3468

East Asian (EAS) AF: 0.306 AC: 1579 AN: 5166

South Asian (SAS) AF: 0.579 AC: 2786 AN: 4812

European-Finnish (FIN) AF: 0.519 AC: 5468 AN: 10528

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.585 AC: 39773 AN: 67932

Other (OTH) AF: 0.555 AC: 1168 AN: 2104

Alfa AF: 0.448 Hom.: 1240

Bravo AF: 0.546

Asia WGS AF: 0.490 AC: 1702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	4.0
DANN	Benign	0.84
PhyloP100		0.045

Splicing

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

Other links and lift over

dbSNP: rs9317760; hg19: chr13-69582685;