11-98172652-A-G

Variant names:

• chr11-98172652-A-G
• rs1941861

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 0.846 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.785 AC: 32583 AN: 41484

American (AMR) AF: 0.836 AC: 12786 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.850 AC: 2951 AN: 3470

East Asian (EAS) AF: 0.966 AC: 4992 AN: 5166

South Asian (SAS) AF: 0.895 AC: 4321 AN: 4830

European-Finnish (FIN) AF: 0.803 AC: 8500 AN: 10586

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.878 AC: 59686 AN: 68014

Other (OTH) AF: 0.842 AC: 1779 AN: 2112

Alfa AF: 0.847 Hom.: 5469

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
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs1941861; hg19: chr11-98043380;