11-61650000-G-A

Position:

• chr11-61650000-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 0.425 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.425 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

Gnomad4 AFR AF: 0.444

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.566

Gnomad4 EAS AF: 0.0565

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.424

Alfa AF: 0.457 Hom.: 33946

Bravo AF: 0.422

Asia WGS AF: 0.178 AC: 623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1692120; hg19: chr11-61417472;