15-78432127-C-T

Variant names:

• chr15-78432127-C-T
• rs1394371

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 0.219 in 152,176 control chromosomes in the GnomAD database, including 4,221 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 0.22 (4221 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 26 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 (NFE) allele frequency at 95% confidence interval = 0.286 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: 0.219 AC: 33303 AN: 152058 Hom.: 4214 Cov.: 33

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.0393

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.219 AC: 33339 AN: 152176 Hom.: 4221 Cov.: 33 AF XY: 0.217 AC XY: 16113 AN XY: 74404

African (AFR) AF: 0.111 AC: 4628 AN: 41540

American (AMR) AF: 0.194 AC: 2970 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1085 AN: 3468

East Asian (EAS) AF: 0.0396 AC: 205 AN: 5182

South Asian (SAS) AF: 0.187 AC: 901 AN: 4828

European-Finnish (FIN) AF: 0.282 AC: 2979 AN: 10568

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19670 AN: 67980

Other (OTH) AF: 0.227 AC: 479 AN: 2112

Alfa AF: 0.261 Hom.: 12599

Bravo AF: 0.208

Asia WGS AF: 0.121 AC: 422 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	0.064
DANN	Benign	0.50
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1394371; hg19: chr15-78724469;