11-98807114-T-G

Variant names:

• chr11-98807114-T-G
• rs334265

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 0.974 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.974 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

Gnomad4 AFR AF: 0.951

Gnomad4 AMR AF: 0.992

Gnomad4 ASJ AF: 0.967

Gnomad4 EAS AF: 0.973

Gnomad4 SAS AF: 0.946

Gnomad4 FIN AF: 0.987

Gnomad4 NFE AF: 0.985

Gnomad4 OTH AF: 0.980

Alfa AF: 0.986 Hom.: 3428

Bravo AF: 0.975

Asia WGS AF: 0.954 AC: 3315 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs334265; hg19: chr11-98677844;