rs10896072

Variant names:

• chr11-65983146-C-G
• rs10896072

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;