11-61650000-G-A

Variant names:

• chr11-61650000-G-A
• rs1692120

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 0.425 in 152,108 control chromosomes in the GnomAD database, including 14,424 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 0.43 (14424 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.309
• Publications: 27 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64662 AN: 151990 Hom.: 14398 Cov.: 33

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.0566

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.425 AC: 64721 AN: 152108 Hom.: 14424 Cov.: 33 AF XY: 0.418 AC XY: 31111 AN XY: 74354

African (AFR) AF: 0.444 AC: 18433 AN: 41488

American (AMR) AF: 0.337 AC: 5151 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1965 AN: 3470

East Asian (EAS) AF: 0.0565 AC: 293 AN: 5184

South Asian (SAS) AF: 0.263 AC: 1268 AN: 4822

European-Finnish (FIN) AF: 0.435 AC: 4596 AN: 10568

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.464 AC: 31566 AN: 67986

Other (OTH) AF: 0.424 AC: 897 AN: 2116

Alfa AF: 0.449 Hom.: 64737

Bravo AF: 0.422

Asia WGS AF: 0.178 AC: 623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.11
DANN	Benign	0.58
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs1692120; hg19: chr11-61417472;