11-98595538-T-C

Position:

• chr11-98595538-T-C

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 0.39 in 151,826 control chromosomes in the GnomAD database, including 11,817 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 0.39 (11817 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.222

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59162 AN: 151708 Hom.: 11809 Cov.: 31

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.390 AC: 59202 AN: 151826 Hom.: 11817 Cov.: 31 AF XY: 0.392 AC XY: 29073 AN XY: 74190

Gnomad4 AFR AF: 0.429

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.447

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.397

Gnomad4 NFE AF: 0.369

Gnomad4 OTH AF: 0.359

Alfa AF: 0.368 Hom.: 15603

Bravo AF: 0.392

Asia WGS AF: 0.417 AC: 1444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.7
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4237591; hg19: chr11-98466268;