11-63411961-T-C

Variant names:

• chr11-63411961-T-C
• rs7104097

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.500 AC: 20316 AN: 40646

American (AMR) AF: 0.443 AC: 6644 AN: 14990

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 603 AN: 3440

East Asian (EAS) AF: 0.821 AC: 4196 AN: 5110

South Asian (SAS) AF: 0.484 AC: 2300 AN: 4752

European-Finnish (FIN) AF: 0.314 AC: 2817 AN: 8958

Middle Eastern (MID) AF: 0.222 AC: 63 AN: 284

European-Non Finnish (NFE) AF: 0.250 AC: 16820 AN: 67218

Other (OTH) AF: 0.386 AC: 800 AN: 2072

Alfa AF: 0.161 Hom.: 347

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
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs7104097; hg19: chr11-63179433;