rs11619878

Variant names:

• chr13-65637888-G-A
• rs11619878

Your query was ambiguous. Multiple possible variants found:

• chr13-65637888-G-A
• chr13-65637888-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 0.471 in 150,904 control chromosomes in the GnomAD database, including 17,326 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 0.47 (17326 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.710
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.52 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: 0.471 AC: 71042 AN: 150792 Hom.: 17312 Cov.: 28

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.0932

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.471 AC: 71107 AN: 150904 Hom.: 17326 Cov.: 28 AF XY: 0.466 AC XY: 34309 AN XY: 73664

African (AFR) AF: 0.437 AC: 17957 AN: 41134

American (AMR) AF: 0.440 AC: 6634 AN: 15082

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1611 AN: 3460

East Asian (EAS) AF: 0.0932 AC: 474 AN: 5084

South Asian (SAS) AF: 0.482 AC: 2299 AN: 4774

European-Finnish (FIN) AF: 0.485 AC: 5064 AN: 10442

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.525 AC: 35498 AN: 67634

Other (OTH) AF: 0.453 AC: 945 AN: 2088

Alfa AF: 0.495 Hom.: 63978

Bravo AF: 0.459

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.74
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs11619878; hg19: chr13-66212020;