11-65889093-C-T

Variant names:

• chr11-65889093-C-T
• rs2231884

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 0.163 in 152,196 control chromosomes in the GnomAD database, including 2,188 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 0.16 (2188 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114
• Publications: 53 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.316 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: 0.163 AC: 24808 AN: 152078 Hom.: 2184 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.163 AC: 24826 AN: 152196 Hom.: 2188 Cov.: 32 AF XY: 0.161 AC XY: 11970 AN XY: 74386

African (AFR) AF: 0.158 AC: 6576 AN: 41542

American (AMR) AF: 0.154 AC: 2356 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 499 AN: 3470

East Asian (EAS) AF: 0.329 AC: 1692 AN: 5150

South Asian (SAS) AF: 0.110 AC: 530 AN: 4828

European-Finnish (FIN) AF: 0.152 AC: 1606 AN: 10596

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11068 AN: 68000

Other (OTH) AF: 0.170 AC: 359 AN: 2112

Alfa AF: 0.164 Hom.: 6018

Bravo AF: 0.164

Asia WGS AF: 0.178 AC: 618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	9.8
DANN	Benign	0.92
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs2231884; hg19: chr11-65656564;