11-63411961-T-C

Variant names:

• chr11-63411961-T-C
• rs7104097

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 0.369 in 148,376 control chromosomes in the GnomAD database, including 11,601 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 0.37 (11601 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.8 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: 0.369 AC: 54732 AN: 148304 Hom.: 11578 Cov.: 30

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.821

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.219

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.369 AC: 54802 AN: 148376 Hom.: 11601 Cov.: 30 AF XY: 0.374 AC XY: 27003 AN XY: 72220

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.443

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.821

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.386

Alfa AF: 0.141 Hom.: 254

Bravo AF: 0.389

Asia WGS AF: 0.635 AC: 2193 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.7
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7104097; hg19: chr11-63179433;