chr13-65523958-T-A

Variant names:

• chr13-65523958-T-A
• rs9317514

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 0.151 in 151,756 control chromosomes in the GnomAD database, including 1,788 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 0.15 (1788 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.194 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: 0.151 AC: 22873 AN: 151640 Hom.: 1788 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.151 AC: 22883 AN: 151756 Hom.: 1788 Cov.: 32 AF XY: 0.152 AC XY: 11288 AN XY: 74154

African (AFR) AF: 0.198 AC: 8170 AN: 41348

American (AMR) AF: 0.121 AC: 1846 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 473 AN: 3464

East Asian (EAS) AF: 0.115 AC: 592 AN: 5152

South Asian (SAS) AF: 0.135 AC: 649 AN: 4800

European-Finnish (FIN) AF: 0.153 AC: 1611 AN: 10528

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9027 AN: 67896

Other (OTH) AF: 0.131 AC: 277 AN: 2108

Alfa AF: 0.0728 Hom.: 83

Bravo AF: 0.150

Asia WGS AF: 0.110 AC: 383 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.2
DANN	Benign	0.58
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs9317514; hg19: chr13-66098090;