rs11246228

Variant names:

• chr11-641563-T-C
• rs11246228

Your query was ambiguous. Multiple possible variants found:

• chr11-641563-T-C
• chr11-641563-T-G

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 0.4 in 152,170 control chromosomes in the GnomAD database, including 12,460 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 0.40 (12460 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.66
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.512 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: 0.400 AC: 60882 AN: 152052 Hom.: 12462 Cov.: 34

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.529

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.400 AC: 60908 AN: 152170 Hom.: 12460 Cov.: 34 AF XY: 0.402 AC XY: 29877 AN XY: 74400

African (AFR) AF: 0.330 AC: 13724 AN: 41526

American (AMR) AF: 0.354 AC: 5411 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1493 AN: 3470

East Asian (EAS) AF: 0.529 AC: 2733 AN: 5168

South Asian (SAS) AF: 0.504 AC: 2430 AN: 4822

European-Finnish (FIN) AF: 0.426 AC: 4513 AN: 10588

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 29146 AN: 67980

Other (OTH) AF: 0.413 AC: 874 AN: 2116

Alfa AF: 0.353 Hom.: 2108

Bravo AF: 0.392

Asia WGS AF: 0.462 AC: 1607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.37
DANN	Benign	0.46
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs11246228; hg19: chr11-641563;