11-61872907-G-A

Variant names:

• chr11-61872907-G-A
• rs174449

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 0.547 in 151,954 control chromosomes in the GnomAD database, including 24,017 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 0.55 (24017 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192
• Publications: 48 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.668 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: 0.548 AC: 83159 AN: 151836 Hom.: 24014 Cov.: 31

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.547 AC: 83188 AN: 151954 Hom.: 24017 Cov.: 31 AF XY: 0.547 AC XY: 40604 AN XY: 74276

African (AFR) AF: 0.387 AC: 16059 AN: 41480

American (AMR) AF: 0.435 AC: 6646 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.649 AC: 2250 AN: 3466

East Asian (EAS) AF: 0.687 AC: 3521 AN: 5124

South Asian (SAS) AF: 0.564 AC: 2715 AN: 4814

European-Finnish (FIN) AF: 0.637 AC: 6734 AN: 10564

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.639 AC: 43364 AN: 67906

Other (OTH) AF: 0.553 AC: 1167 AN: 2110

Alfa AF: 0.598 Hom.: 75912

Bravo AF: 0.527

Asia WGS AF: 0.585 AC: 2036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.3
DANN	Benign	0.68
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs174449; hg19: chr11-61640379;