chr15-74710710-T-C

Variant names:

• chr15-74710710-T-C
• rs1456432

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 0.302 in 152,048 control chromosomes in the GnomAD database, including 9,302 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 0.30 (9302 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.52 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: 0.301 AC: 45776 AN: 151930 Hom.: 9257 Cov.: 31

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.302 AC: 45892 AN: 152048 Hom.: 9302 Cov.: 31 AF XY: 0.306 AC XY: 22735 AN XY: 74332

African (AFR) AF: 0.526 AC: 21820 AN: 41466

American (AMR) AF: 0.414 AC: 6313 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 842 AN: 3470

East Asian (EAS) AF: 0.522 AC: 2693 AN: 5156

South Asian (SAS) AF: 0.351 AC: 1688 AN: 4812

European-Finnish (FIN) AF: 0.144 AC: 1529 AN: 10582

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10061 AN: 67986

Other (OTH) AF: 0.300 AC: 635 AN: 2114

Alfa AF: 0.0723 Hom.: 91

Bravo AF: 0.330

Asia WGS AF: 0.499 AC: 1730 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.66
DANN	Benign	0.33
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1456432; hg19: chr15-75003051;