11-97866007-G-T

Position:

• chr11-97866007-G-T

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 0.295 in 151,584 control chromosomes in the GnomAD database, including 6,947 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 0.29 (6947 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.282

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.341 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: 0.295 AC: 44674 AN: 151468 Hom.: 6941 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.295 AC: 44696 AN: 151584 Hom.: 6947 Cov.: 32 AF XY: 0.293 AC XY: 21684 AN XY: 74040

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.335

Alfa AF: 0.338 Hom.: 10715

Bravo AF: 0.289

Asia WGS AF: 0.184 AC: 637 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.25
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: rs949175; hg19: chr11-97737007; COSMIC: COSV51267247;