rs1690593

Variant names:

• chr11-97177674-G-A
• rs1690593

Your query was ambiguous. Multiple possible variants found:

• chr11-97177674-G-A
• chr11-97177674-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.578 in 151,696 control chromosomes in the GnomAD database, including 25,629 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 0.58 (25629 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.766
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.653 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: 0.578 AC: 87658 AN: 151576 Hom.: 25613 Cov.: 31

Gnomad AFR AF: 0.660

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.578 AC: 87721 AN: 151696 Hom.: 25629 Cov.: 31 AF XY: 0.574 AC XY: 42566 AN XY: 74096

African (AFR) AF: 0.659 AC: 27210 AN: 41266

American (AMR) AF: 0.561 AC: 8547 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2027 AN: 3468

East Asian (EAS) AF: 0.623 AC: 3198 AN: 5134

South Asian (SAS) AF: 0.396 AC: 1908 AN: 4818

European-Finnish (FIN) AF: 0.535 AC: 5632 AN: 10532

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.548 AC: 37263 AN: 67942

Other (OTH) AF: 0.558 AC: 1176 AN: 2108

Alfa AF: 0.571 Hom.: 3147

Bravo AF: 0.588

Asia WGS AF: 0.434 AC: 1507 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	1.1
DANN	Benign	0.80
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs1690593; hg19: chr11-97048674;