rs2069514

Variant names:

• chr15-74745879-G-A
• rs2069514

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 0.127 in 152,038 control chromosomes in the GnomAD database, including 2,533 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 0.13 (2533 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.970
• Publications: 130 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 = 0.273 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: 0.127 AC: 19233 AN: 151920 Hom.: 2514 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.0337

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.0820

Gnomad FIN AF: 0.0490

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0130

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.127 AC: 19303 AN: 152038 Hom.: 2533 Cov.: 32 AF XY: 0.131 AC XY: 9698 AN XY: 74302

African (AFR) AF: 0.277 AC: 11493 AN: 41430

American (AMR) AF: 0.272 AC: 4146 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0337 AC: 117 AN: 3470

East Asian (EAS) AF: 0.265 AC: 1367 AN: 5166

South Asian (SAS) AF: 0.0825 AC: 397 AN: 4814

European-Finnish (FIN) AF: 0.0490 AC: 519 AN: 10584

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0130 AC: 881 AN: 67996

Other (OTH) AF: 0.116 AC: 244 AN: 2112

Alfa AF: 0.0727 Hom.: 163

Bravo AF: 0.153

Asia WGS AF: 0.193 AC: 671 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	0.36
DANN	Benign	0.77
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs2069514; hg19: chr15-75038220;