rs2219854

Variant names:

• chr15-94135874-T-C
• rs2219854

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 0.191 in 152,178 control chromosomes in the GnomAD database, including 3,839 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 0.19 (3839 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.329
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28944 AN: 152062 Hom.: 3823 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.0502

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.0627

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.191 AC: 28995 AN: 152178 Hom.: 3839 Cov.: 32 AF XY: 0.185 AC XY: 13730 AN XY: 74402

African (AFR) AF: 0.379 AC: 15695 AN: 41466

American (AMR) AF: 0.129 AC: 1967 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 540 AN: 3468

East Asian (EAS) AF: 0.0503 AC: 261 AN: 5188

South Asian (SAS) AF: 0.160 AC: 771 AN: 4822

European-Finnish (FIN) AF: 0.0627 AC: 666 AN: 10616

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8446 AN: 68016

Other (OTH) AF: 0.182 AC: 385 AN: 2114

Alfa AF: 0.143 Hom.: 3115

Bravo AF: 0.202

Asia WGS AF: 0.115 AC: 402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.5
DANN	Benign	0.83
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs2219854; hg19: chr15-94679103;