11-65651893-G-C

Variant names:

• chr11-65651893-G-C
• rs1466462

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 0.338 in 152,234 control chromosomes in the GnomAD database, including 9,238 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 0.34 (9238 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.188
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.38 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: 0.338 AC: 51388 AN: 152116 Hom.: 9233 Cov.: 33

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.338 AC: 51425 AN: 152234 Hom.: 9238 Cov.: 33 AF XY: 0.343 AC XY: 25541 AN XY: 74416

African (AFR) AF: 0.254 AC: 10570 AN: 41534

American (AMR) AF: 0.261 AC: 3999 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1416 AN: 3464

East Asian (EAS) AF: 0.211 AC: 1096 AN: 5186

South Asian (SAS) AF: 0.340 AC: 1639 AN: 4824

European-Finnish (FIN) AF: 0.520 AC: 5506 AN: 10598

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.384 AC: 26142 AN: 68012

Other (OTH) AF: 0.325 AC: 687 AN: 2112

Alfa AF: 0.276 Hom.: 793

Bravo AF: 0.309

Asia WGS AF: 0.258 AC: 899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.0
DANN	Benign	0.73
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs1466462; hg19: chr11-65419364;