11-38180741-A-G

Variant names:

• chr11-38180741-A-G
• rs2861126

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 0.924 in 152,146 control chromosomes in the GnomAD database, including 65,502 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 0.92 (65502 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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: 0.924 AC: 140499 AN: 152028 Hom.: 65468 Cov.: 31

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.987

Gnomad AMR AF: 0.960

Gnomad ASJ AF: 0.992

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.942

Gnomad FIN AF: 0.968

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.982

Gnomad OTH AF: 0.941

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

GnomAD4 genome AF: 0.924 AC: 140589 AN: 152146 Hom.: 65502 Cov.: 31 AF XY: 0.926 AC XY: 68864 AN XY: 74402

Gnomad4 AFR AF: 0.787

Gnomad4 AMR AF: 0.961

Gnomad4 ASJ AF: 0.992

Gnomad4 EAS AF: 0.982

Gnomad4 SAS AF: 0.941

Gnomad4 FIN AF: 0.968

Gnomad4 NFE AF: 0.982

Gnomad4 OTH AF: 0.941

Alfa AF: 0.951 Hom.: 3830

Bravo AF: 0.918

Asia WGS AF: 0.945 AC: 3288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.31
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2861126; hg19: chr11-38202291;