11-65983146-C-G

Variant names:

• chr11-65983146-C-G
• rs10896072

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0727 in 152,038 control chromosomes in the GnomAD database, including 564 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 0.073 (564 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.834
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0728 AC: 11067 AN: 151920 Hom.: 564 Cov.: 31

Gnomad AFR AF: 0.0172

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0665

Gnomad ASJ AF: 0.0783

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0788

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.0778

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

GnomAD4 genome AF: 0.0727 AC: 11060 AN: 152038 Hom.: 564 Cov.: 31 AF XY: 0.0745 AC XY: 5536 AN XY: 74320

African (AFR) AF: 0.0172 AC: 712 AN: 41496

American (AMR) AF: 0.0664 AC: 1013 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0783 AC: 272 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5176

South Asian (SAS) AF: 0.0786 AC: 379 AN: 4820

European-Finnish (FIN) AF: 0.135 AC: 1417 AN: 10528

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 7017 AN: 67974

Other (OTH) AF: 0.0765 AC: 161 AN: 2104

Alfa AF: 0.0938 Hom.: 112

Bravo AF: 0.0643

Asia WGS AF: 0.0320 AC: 111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	15
DANN	Benign	0.88
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs10896072; hg19: chr11-65750617;