rs10796849

Positions:

• chr11-69787644-C-G
• chr11-69787644-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.692 in 152,026 control chromosomes in the GnomAD database, including 39,470 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 0.69 (39470 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.437

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.849 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.692 AC: 105109 AN: 151908 Hom.: 39474 Cov.: 32

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.954

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.821

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.862

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.855

Gnomad OTH AF: 0.725

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

GnomAD4 genome AF: 0.692 AC: 105126 AN: 152026 Hom.: 39470 Cov.: 32 AF XY: 0.691 AC XY: 51305 AN XY: 74294

Gnomad4 AFR AF: 0.402

Gnomad4 AMR AF: 0.624

Gnomad4 ASJ AF: 0.821

Gnomad4 EAS AF: 0.570

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.862

Gnomad4 NFE AF: 0.854

Gnomad4 OTH AF: 0.724

Alfa AF: 0.763 Hom.: 5809

Bravo AF: 0.662

Asia WGS AF: 0.640 AC: 2226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10796849; hg19: chr11-69602412;