11-48261740-A-T

Position:

• chr11-48261740-A-T

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 0.69 in 152,060 control chromosomes in the GnomAD database, including 36,948 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 0.69 (36948 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.779

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.751 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: 0.690 AC: 104824 AN: 151942 Hom.: 36935 Cov.: 32

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.835

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.577

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.757

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.690 AC: 104875 AN: 152060 Hom.: 36948 Cov.: 32 AF XY: 0.689 AC XY: 51231 AN XY: 74346

Gnomad4 AFR AF: 0.559

Gnomad4 AMR AF: 0.737

Gnomad4 ASJ AF: 0.694

Gnomad4 EAS AF: 0.578

Gnomad4 SAS AF: 0.546

Gnomad4 FIN AF: 0.811

Gnomad4 NFE AF: 0.757

Gnomad4 OTH AF: 0.681

Alfa AF: 0.730 Hom.: 5125

Bravo AF: 0.682

Asia WGS AF: 0.514 AC: 1788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.94
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7106648; hg19: chr11-48283292;