11-61869585-G-A

Position:

• chr11-61869585-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.371

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.681

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.558

Gnomad4 NFE AF: 0.543

Gnomad4 OTH AF: 0.479

Alfa AF: 0.490 Hom.: 3023

Bravo AF: 0.465

Asia WGS AF: 0.546 AC: 1901 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs174626; hg19: chr11-61637057;