rs1790137

Variant names:

• chr11-107681196-C-A
• rs1790137

Your query was ambiguous. Multiple possible variants found:

• chr11-107681196-C-A
• chr11-107681196-C-G
• chr11-107681196-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 0.771 in 152,148 control chromosomes in the GnomAD database, including 45,863 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 0.77 (45863 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.785

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.884 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: 0.771 AC: 117179 AN: 152030 Hom.: 45810 Cov.: 32

Gnomad AFR AF: 0.892

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.861

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.771 AC: 117290 AN: 152148 Hom.: 45863 Cov.: 32 AF XY: 0.773 AC XY: 57473 AN XY: 74386

Gnomad4 AFR AF: 0.892

Gnomad4 AMR AF: 0.788

Gnomad4 ASJ AF: 0.668

Gnomad4 EAS AF: 0.861

Gnomad4 SAS AF: 0.640

Gnomad4 FIN AF: 0.760

Gnomad4 NFE AF: 0.704

Gnomad4 OTH AF: 0.765

Alfa AF: 0.720 Hom.: 19376

Bravo AF: 0.786

Asia WGS AF: 0.748 AC: 2602 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.43
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1790137; hg19: chr11-107551922;