chr2-113078771-C-T

Variant names:

• chr2-113078771-C-T
• rs6759676

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 0.559 in 151,932 control chromosomes in the GnomAD database, including 24,282 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 0.56 (24282 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 17 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84927 AN: 151814 Hom.: 24253 Cov.: 31

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.559 AC: 84991 AN: 151932 Hom.: 24282 Cov.: 31 AF XY: 0.556 AC XY: 41303 AN XY: 74268

African (AFR) AF: 0.578 AC: 23943 AN: 41396

American (AMR) AF: 0.566 AC: 8641 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1972 AN: 3470

East Asian (EAS) AF: 0.161 AC: 835 AN: 5172

South Asian (SAS) AF: 0.651 AC: 3133 AN: 4816

European-Finnish (FIN) AF: 0.557 AC: 5874 AN: 10548

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.567 AC: 38531 AN: 67956

Other (OTH) AF: 0.577 AC: 1215 AN: 2104

Alfa AF: 0.569 Hom.: 20162

Bravo AF: 0.559

Asia WGS AF: 0.469 AC: 1632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.21
DANN	Benign	0.60
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs6759676; hg19: chr2-113836348;