11-97996937-T-C

Variant names:

• chr11-97996937-T-C
• rs4590838

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 0.789 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.598 AC: 24802 AN: 41464

American (AMR) AF: 0.867 AC: 13251 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.858 AC: 2976 AN: 3468

East Asian (EAS) AF: 0.919 AC: 4752 AN: 5170

South Asian (SAS) AF: 0.849 AC: 4097 AN: 4826

European-Finnish (FIN) AF: 0.861 AC: 9115 AN: 10590

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.859 AC: 58368 AN: 67950

Other (OTH) AF: 0.809 AC: 1708 AN: 2110

Alfa AF: 0.832 Hom.: 161619

Bravo AF: 0.780

Asia WGS AF: 0.869 AC: 3023 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.4
DANN	Benign	0.65
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs4590838; hg19: chr11-97867665;