11-98807114-T-G

Variant names:

• chr11-98807114-T-G
• rs334265

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 0.974 in 151,570 control chromosomes in the GnomAD database, including 71,946 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 (71946 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.979 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.974 AC: 147550 AN: 151452 Hom.: 71890 Cov.: 31

Gnomad AFR AF: 0.951

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.992

Gnomad ASJ AF: 0.967

Gnomad EAS AF: 0.972

Gnomad SAS AF: 0.946

Gnomad FIN AF: 0.987

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.985

Gnomad OTH AF: 0.979

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

GnomAD4 genome AF: 0.974 AC: 147666 AN: 151570 Hom.: 71946 Cov.: 31 AF XY: 0.974 AC XY: 72165 AN XY: 74092

African (AFR) AF: 0.951 AC: 39431 AN: 41472

American (AMR) AF: 0.992 AC: 15088 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.967 AC: 3345 AN: 3460

East Asian (EAS) AF: 0.973 AC: 5009 AN: 5150

South Asian (SAS) AF: 0.946 AC: 4546 AN: 4806

European-Finnish (FIN) AF: 0.987 AC: 10471 AN: 10612

Middle Eastern (MID) AF: 0.983 AC: 289 AN: 294

European-Non Finnish (NFE) AF: 0.985 AC: 66516 AN: 67554

Other (OTH) AF: 0.980 AC: 2059 AN: 2102

Alfa AF: 0.983 Hom.: 3784

Bravo AF: 0.975

Asia WGS AF: 0.954 AC: 3315 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.62
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs334265; hg19: chr11-98677844;