rs2219994

Variant names:

• chr15-60152792-C-T
• rs2219994

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.102 in 152,064 control chromosomes in the GnomAD database, including 2,225 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 0.10 (2225 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.197

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.315 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: 0.102 AC: 15435 AN: 151946 Hom.: 2208 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0441

Gnomad ASJ AF: 0.0432

Gnomad EAS AF: 0.00868

Gnomad SAS AF: 0.0114

Gnomad FIN AF: 0.0191

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0142

Gnomad OTH AF: 0.0872

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

GnomAD4 genome AF: 0.102 AC: 15495 AN: 152064 Hom.: 2225 Cov.: 32 AF XY: 0.0995 AC XY: 7399 AN XY: 74336

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.0440

Gnomad4 ASJ AF: 0.0432

Gnomad4 EAS AF: 0.00870

Gnomad4 SAS AF: 0.0110

Gnomad4 FIN AF: 0.0191

Gnomad4 NFE AF: 0.0142

Gnomad4 OTH AF: 0.0863

Alfa AF: 0.0536 Hom.: 225

Bravo AF: 0.114

Asia WGS AF: 0.0360 AC: 127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2219994; hg19: chr15-60444991;