3-51720100-T-C

Variant names:

• chr3-51720100-T-C
• rs12487957

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 0.0614 in 152,320 control chromosomes in the GnomAD database, including 826 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 0.061 (826 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.520
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.311 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: 0.0614 AC: 9341 AN: 152202 Hom.: 822 Cov.: 32

Gnomad AFR AF: 0.0498

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.0222

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.0536

Gnomad FIN AF: 0.0320

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0204

Gnomad OTH AF: 0.0535

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

GnomAD4 genome AF: 0.0614 AC: 9347 AN: 152320 Hom.: 826 Cov.: 32 AF XY: 0.0656 AC XY: 4885 AN XY: 74482

African (AFR) AF: 0.0500 AC: 2077 AN: 41566

American (AMR) AF: 0.217 AC: 3313 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0222 AC: 77 AN: 3470

East Asian (EAS) AF: 0.324 AC: 1679 AN: 5184

South Asian (SAS) AF: 0.0534 AC: 258 AN: 4830

European-Finnish (FIN) AF: 0.0320 AC: 340 AN: 10620

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0204 AC: 1388 AN: 68034

Other (OTH) AF: 0.0525 AC: 111 AN: 2114

Alfa AF: 0.0649 Hom.: 707

Bravo AF: 0.0785

Asia WGS AF: 0.151 AC: 525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.75
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs12487957; hg19: chr3-51754116;