15-100711514-T-C

Variant names:

• chr15-100711514-T-C
• rs184234

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 0.206 in 152,142 control chromosomes in the GnomAD database, including 3,555 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 0.21 (3555 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31330 AN: 152024 Hom.: 3552 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.0410

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.206 AC: 31343 AN: 152142 Hom.: 3555 Cov.: 32 AF XY: 0.203 AC XY: 15126 AN XY: 74364

African (AFR) AF: 0.149 AC: 6175 AN: 41524

American (AMR) AF: 0.223 AC: 3407 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 629 AN: 3466

East Asian (EAS) AF: 0.0409 AC: 212 AN: 5178

South Asian (SAS) AF: 0.134 AC: 644 AN: 4812

European-Finnish (FIN) AF: 0.200 AC: 2120 AN: 10578

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.257 AC: 17502 AN: 67980

Other (OTH) AF: 0.204 AC: 431 AN: 2110

Alfa AF: 0.237 Hom.: 9543

Bravo AF: 0.207

Asia WGS AF: 0.0880 AC: 308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.9
DANN	Benign	0.49
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs184234; hg19: chr15-101251719;