rs10896072

Positions:

• chr11-65983146-C-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.0172

Gnomad4 AMR AF: 0.0664

Gnomad4 ASJ AF: 0.0783

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0786

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.0765

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10896072; hg19: chr11-65750617;