rs1152620

Variant names:

• chr11-65489858-A-G
• rs1152620

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 0.305 in 151,756 control chromosomes in the GnomAD database, including 7,755 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 0.30 (7755 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.44 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: 0.305 AC: 46198 AN: 151638 Hom.: 7753 Cov.: 31

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.305 AC: 46232 AN: 151756 Hom.: 7755 Cov.: 31 AF XY: 0.299 AC XY: 22196 AN XY: 74138

African (AFR) AF: 0.392 AC: 16214 AN: 41340

American (AMR) AF: 0.396 AC: 6050 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 893 AN: 3464

East Asian (EAS) AF: 0.456 AC: 2345 AN: 5146

South Asian (SAS) AF: 0.237 AC: 1138 AN: 4794

European-Finnish (FIN) AF: 0.144 AC: 1520 AN: 10548

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17018 AN: 67898

Other (OTH) AF: 0.286 AC: 601 AN: 2102

Alfa AF: 0.272 Hom.: 9748

Bravo AF: 0.336

Asia WGS AF: 0.322 AC: 1120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.29
DANN	Benign	0.51
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1152620; hg19: chr11-65257329;