rs1940392

chr11-111906122-G-Achr11-111906122-G-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 0.714 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.865

Gnomad4 AMR AF: 0.723

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.767

Gnomad4 SAS AF: 0.640

Gnomad4 FIN AF: 0.640

Gnomad4 NFE AF: 0.636

Gnomad4 OTH AF: 0.699

Alfa AF: 0.682 Hom.: 4496

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1940392; hg19: chr11-111776846;