chr11-102551820-T-C

Variant names:

• chr11-102551820-T-C
• rs7947031

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 0.228 in 152,056 control chromosomes in the GnomAD database, including 4,288 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 0.23 (4288 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.419
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.314 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: 0.228 AC: 34648 AN: 151938 Hom.: 4269 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.228 AC: 34716 AN: 152056 Hom.: 4288 Cov.: 32 AF XY: 0.235 AC XY: 17442 AN XY: 74314

African (AFR) AF: 0.318 AC: 13192 AN: 41446

American (AMR) AF: 0.230 AC: 3514 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 685 AN: 3470

East Asian (EAS) AF: 0.313 AC: 1617 AN: 5172

South Asian (SAS) AF: 0.174 AC: 837 AN: 4818

European-Finnish (FIN) AF: 0.243 AC: 2571 AN: 10580

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11646 AN: 67992

Other (OTH) AF: 0.217 AC: 458 AN: 2112

Alfa AF: 0.187 Hom.: 5188

Bravo AF: 0.234

Asia WGS AF: 0.232 AC: 806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.7
DANN	Benign	0.83
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs7947031; hg19: chr11-102422551;