11-98927054-A-T

Variant names:

• chr11-98927054-A-T
• rs1026593

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 0.946 in 152,152 control chromosomes in the GnomAD database, including 68,127 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 0.95 (68127 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.747
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.978 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: 0.946 AC: 143802 AN: 152034 Hom.: 68073 Cov.: 33

Gnomad AFR AF: 0.986

Gnomad AMI AF: 0.957

Gnomad AMR AF: 0.957

Gnomad ASJ AF: 0.920

Gnomad EAS AF: 0.897

Gnomad SAS AF: 0.916

Gnomad FIN AF: 0.965

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.923

Gnomad OTH AF: 0.946

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

GnomAD4 genome AF: 0.946 AC: 143914 AN: 152152 Hom.: 68127 Cov.: 33 AF XY: 0.947 AC XY: 70400 AN XY: 74376

African (AFR) AF: 0.986 AC: 40989 AN: 41558

American (AMR) AF: 0.957 AC: 14591 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.920 AC: 3191 AN: 3470

East Asian (EAS) AF: 0.897 AC: 4636 AN: 5166

South Asian (SAS) AF: 0.915 AC: 4410 AN: 4818

European-Finnish (FIN) AF: 0.965 AC: 10247 AN: 10620

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.923 AC: 62708 AN: 67952

Other (OTH) AF: 0.944 AC: 1995 AN: 2114

Alfa AF: 0.928 Hom.: 3078

Bravo AF: 0.947

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.16
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs1026593; hg19: chr11-98797784;