7-114762278-T-C

Variant names:

• chr7-114762278-T-C
• rs12533049

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 0.593 in 152,100 control chromosomes in the GnomAD database, including 31,005 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 0.59 (31005 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.783 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: 0.593 AC: 90196 AN: 151982 Hom.: 30991 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.593 AC: 90228 AN: 152100 Hom.: 31005 Cov.: 32 AF XY: 0.591 AC XY: 43946 AN XY: 74334

African (AFR) AF: 0.250 AC: 10354 AN: 41470

American (AMR) AF: 0.620 AC: 9468 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.696 AC: 2416 AN: 3472

East Asian (EAS) AF: 0.267 AC: 1382 AN: 5182

South Asian (SAS) AF: 0.573 AC: 2764 AN: 4822

European-Finnish (FIN) AF: 0.766 AC: 8108 AN: 10586

Middle Eastern (MID) AF: 0.589 AC: 172 AN: 292

European-Non Finnish (NFE) AF: 0.788 AC: 53600 AN: 67984

Other (OTH) AF: 0.621 AC: 1311 AN: 2112

Alfa AF: 0.617 Hom.: 7840

Bravo AF: 0.566

Asia WGS AF: 0.450 AC: 1567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.3
DANN	Benign	0.82
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs12533049; hg19: chr7-114402333;