chr11-61869585-G-A

Variant names:

• chr11-61869585-G-A
• rs174626

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 0.484 in 151,824 control chromosomes in the GnomAD database, including 18,560 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 0.48 (18560 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.445
• Publications: 18 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 (EAS) allele frequency at 95% confidence interval = 0.662 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: 0.484 AC: 73460 AN: 151706 Hom.: 18565 Cov.: 31

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.484 AC: 73462 AN: 151824 Hom.: 18560 Cov.: 31 AF XY: 0.486 AC XY: 36087 AN XY: 74224

African (AFR) AF: 0.378 AC: 15607 AN: 41334

American (AMR) AF: 0.371 AC: 5668 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1737 AN: 3470

East Asian (EAS) AF: 0.681 AC: 3499 AN: 5140

South Asian (SAS) AF: 0.518 AC: 2493 AN: 4812

European-Finnish (FIN) AF: 0.558 AC: 5875 AN: 10538

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.543 AC: 36925 AN: 67954

Other (OTH) AF: 0.479 AC: 1010 AN: 2110

Alfa AF: 0.473 Hom.: 7290

Bravo AF: 0.465

Asia WGS AF: 0.546 AC: 1901 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.9
DANN	Benign	0.69
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs174626; hg19: chr11-61637057;