rs10790268

Positions:

• chr11-118858682-A-G
• chr11-118858682-A-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 0.802 in 150,956 control chromosomes in the GnomAD database, including 48,613 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 0.80 (48613 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.613

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.852 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: 0.802 AC: 121002 AN: 150838 Hom.: 48558 Cov.: 26

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.828

Gnomad ASJ AF: 0.824

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.839

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.822

Gnomad NFE AF: 0.802

Gnomad OTH AF: 0.816

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

GnomAD4 genome AF: 0.802 AC: 121114 AN: 150956 Hom.: 48613 Cov.: 26 AF XY: 0.804 AC XY: 59272 AN XY: 73678

Gnomad4 AFR AF: 0.772

Gnomad4 AMR AF: 0.828

Gnomad4 ASJ AF: 0.824

Gnomad4 EAS AF: 0.874

Gnomad4 SAS AF: 0.838

Gnomad4 FIN AF: 0.829

Gnomad4 NFE AF: 0.802

Gnomad4 OTH AF: 0.818

Alfa AF: 0.738 Hom.: 2200

Bravo AF: 0.804

Asia WGS AF: 0.849 AC: 2948 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.88
DANN	Benign	0.13

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10790268; hg19: chr11-118729391;