rs11619306

Variant names:

• chr13-29731754-C-G
• rs11619306

Your query was ambiguous. Multiple possible variants found:

• chr13-29731754-C-G
• chr13-29731754-C-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 0.386 in 151,954 control chromosomes in the GnomAD database, including 12,251 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 0.39 (12251 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.488 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: 0.386 AC: 58661 AN: 151836 Hom.: 12241 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.386 AC: 58684 AN: 151954 Hom.: 12251 Cov.: 32 AF XY: 0.391 AC XY: 29018 AN XY: 74266

African (AFR) AF: 0.232 AC: 9598 AN: 41426

American (AMR) AF: 0.497 AC: 7592 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1420 AN: 3468

East Asian (EAS) AF: 0.255 AC: 1320 AN: 5172

South Asian (SAS) AF: 0.414 AC: 1993 AN: 4818

European-Finnish (FIN) AF: 0.464 AC: 4887 AN: 10536

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.451 AC: 30662 AN: 67952

Other (OTH) AF: 0.391 AC: 825 AN: 2108

Alfa AF: 0.419 Hom.: 1745

Bravo AF: 0.381

Asia WGS AF: 0.308 AC: 1071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.0
DANN	Benign	0.43
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs11619306; hg19: chr13-30305891;