11-102878215-A-G

Variant names:

• chr11-102878215-A-G
• rs636648

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 0.103 in 152,224 control chromosomes in the GnomAD database, including 1,168 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 0.10 (1168 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.407
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.207 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: 0.103 AC: 15731 AN: 152106 Hom.: 1163 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.0745

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.0920

Gnomad FIN AF: 0.0406

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0532

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.103 AC: 15737 AN: 152224 Hom.: 1168 Cov.: 32 AF XY: 0.101 AC XY: 7536 AN XY: 74438

African (AFR) AF: 0.210 AC: 8726 AN: 41498

American (AMR) AF: 0.0743 AC: 1136 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 441 AN: 3472

East Asian (EAS) AF: 0.109 AC: 563 AN: 5180

South Asian (SAS) AF: 0.0908 AC: 438 AN: 4824

European-Finnish (FIN) AF: 0.0406 AC: 431 AN: 10620

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0532 AC: 3616 AN: 68020

Other (OTH) AF: 0.111 AC: 234 AN: 2116

Alfa AF: 0.0913 Hom.: 154

Bravo AF: 0.111

Asia WGS AF: 0.109 AC: 381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.0
DANN	Benign	0.40
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs636648; hg19: chr11-102748945;