11-97996937-T-C

Position:

• chr11-97996937-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 0.789 in 152,060 control chromosomes in the GnomAD database, including 48,503 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 0.79 (48503 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.648

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.790 AC: 119973 AN: 151942 Hom.: 48482 Cov.: 33

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.858

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.849

Gnomad FIN AF: 0.861

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.859

Gnomad OTH AF: 0.811

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

GnomAD4 genome AF: 0.789 AC: 120036 AN: 152060 Hom.: 48503 Cov.: 33 AF XY: 0.792 AC XY: 58878 AN XY: 74300

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.867

Gnomad4 ASJ AF: 0.858

Gnomad4 EAS AF: 0.919

Gnomad4 SAS AF: 0.849

Gnomad4 FIN AF: 0.861

Gnomad4 NFE AF: 0.859

Gnomad4 OTH AF: 0.809

Alfa AF: 0.851 Hom.: 113124

Bravo AF: 0.780

Asia WGS AF: 0.869 AC: 3023 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.4
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4590838; hg19: chr11-97867665;