chr11-98024776-G-A

Variant names:

• chr11-98024776-G-A
• rs1293651

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 0.975 in 144,800 control chromosomes in the GnomAD database, including 68,918 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 0.97 (68918 hom., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 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: 0.975 AC: 141102 AN: 144756 Hom.: 68901 Cov.: 23

Gnomad AFR AF: 0.911

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.993

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.990

Gnomad NFE AF: 0.999

Gnomad OTH AF: 0.979

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

GnomAD4 genome AF: 0.975 AC: 141140 AN: 144800 Hom.: 68918 Cov.: 23 AF XY: 0.975 AC XY: 68067 AN XY: 69814

African (AFR) AF: 0.911 AC: 35384 AN: 38830

American (AMR) AF: 0.993 AC: 14265 AN: 14360

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3454 AN: 3454

East Asian (EAS) AF: 1.00 AC: 4914 AN: 4914

South Asian (SAS) AF: 1.00 AC: 4694 AN: 4694

European-Finnish (FIN) AF: 0.997 AC: 8066 AN: 8092

Middle Eastern (MID) AF: 0.993 AC: 278 AN: 280

European-Non Finnish (NFE) AF: 0.999 AC: 67208 AN: 67256

Other (OTH) AF: 0.979 AC: 1968 AN: 2010

Alfa AF: 0.919 Hom.: 1079

Bravo AF: 0.972

Asia WGS AF: 0.974 AC: 3280 AN: 3366

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.90
DANN	Benign	0.63
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs1293651; hg19: chr11-97895504;