rs1941861

chr11-98172652-A-Gchr11-98172652-A-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 0.846 in 152,158 control chromosomes in the GnomAD database, including 54,608 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 0.85 (54608 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.944 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: 0.846 AC: 128598 AN: 152038 Hom.: 54565 Cov.: 32

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.837

Gnomad ASJ AF: 0.850

Gnomad EAS AF: 0.966

Gnomad SAS AF: 0.894

Gnomad FIN AF: 0.803

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.878

Gnomad OTH AF: 0.841

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

GnomAD4 genome AF: 0.846 AC: 128691 AN: 152158 Hom.: 54608 Cov.: 32 AF XY: 0.844 AC XY: 62815 AN XY: 74392

Gnomad4 AFR AF: 0.785

Gnomad4 AMR AF: 0.836

Gnomad4 ASJ AF: 0.850

Gnomad4 EAS AF: 0.966

Gnomad4 SAS AF: 0.895

Gnomad4 FIN AF: 0.803

Gnomad4 NFE AF: 0.878

Gnomad4 OTH AF: 0.842

Alfa AF: 0.849 Hom.: 5216

Bravo AF: 0.843

Asia WGS AF: 0.908 AC: 3157 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	3.3
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1941861; hg19: chr11-98043380;