rs1940392

Variant names:

• chr11-111906122-G-A
• rs1940392

Your query was ambiguous. Multiple possible variants found:

• chr11-111906122-G-A
• chr11-111906122-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 0.714 in 152,072 control chromosomes in the GnomAD database, including 39,527 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 0.71 (39527 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.858 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: 0.714 AC: 108445 AN: 151954 Hom.: 39491 Cov.: 31

Gnomad AFR AF: 0.865

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.767

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.701

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

GnomAD4 genome AF: 0.714 AC: 108535 AN: 152072 Hom.: 39527 Cov.: 31 AF XY: 0.716 AC XY: 53242 AN XY: 74322

African (AFR) AF: 0.865 AC: 35917 AN: 41504

American (AMR) AF: 0.723 AC: 11056 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2218 AN: 3470

East Asian (EAS) AF: 0.767 AC: 3977 AN: 5186

South Asian (SAS) AF: 0.640 AC: 3083 AN: 4818

European-Finnish (FIN) AF: 0.640 AC: 6745 AN: 10546

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.636 AC: 43187 AN: 67952

Other (OTH) AF: 0.699 AC: 1478 AN: 2114

Alfa AF: 0.689 Hom.: 4776

Bravo AF: 0.728

Asia WGS AF: 0.688 AC: 2393 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.7
DANN	Benign	0.78
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs1940392; hg19: chr11-111776846;