rs11618775

Variant names:

• chr13-26952128-G-A
• rs11618775

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 0.19 in 152,222 control chromosomes in the GnomAD database, including 3,256 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 0.19 (3256 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.301
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.26 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: 0.190 AC: 28941 AN: 152104 Hom.: 3256 Cov.: 33

Gnomad AFR AF: 0.0906

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.0284

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.190 AC: 28950 AN: 152222 Hom.: 3256 Cov.: 33 AF XY: 0.188 AC XY: 13960 AN XY: 74410

African (AFR) AF: 0.0905 AC: 3762 AN: 41566

American (AMR) AF: 0.140 AC: 2142 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 588 AN: 3466

East Asian (EAS) AF: 0.0286 AC: 148 AN: 5166

South Asian (SAS) AF: 0.242 AC: 1166 AN: 4826

European-Finnish (FIN) AF: 0.225 AC: 2380 AN: 10588

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.263 AC: 17896 AN: 68000

Other (OTH) AF: 0.191 AC: 402 AN: 2106

Alfa AF: 0.244 Hom.: 13222

Bravo AF: 0.176

Asia WGS AF: 0.129 AC: 449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.5
DANN	Benign	0.73
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs11618775; hg19: chr13-27526265;