11-61092414-T-G

Position:

• chr11-61092414-T-G

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 0.417 in 151,968 control chromosomes in the GnomAD database, including 14,402 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 0.42 (14402 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63335 AN: 151850 Hom.: 14389 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.417 AC: 63378 AN: 151968 Hom.: 14402 Cov.: 32 AF XY: 0.430 AC XY: 31898 AN XY: 74260

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.923

Gnomad4 SAS AF: 0.601

Gnomad4 FIN AF: 0.538

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.397

Alfa AF: 0.320 Hom.: 1992

Bravo AF: 0.412

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.0060
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs612415; hg19: chr11-60859886;