rs2102264

Variant names:

• chr15-78436266-A-G
• rs2102264

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 0.0747 in 152,116 control chromosomes in the GnomAD database, including 1,373 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 0.075 (1373 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.248 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: 0.0746 AC: 11340 AN: 151998 Hom.: 1373 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0311

Gnomad ASJ AF: 0.0300

Gnomad EAS AF: 0.0214

Gnomad SAS AF: 0.00498

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00138

Gnomad OTH AF: 0.0497

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

GnomAD4 genome AF: 0.0747 AC: 11361 AN: 152116 Hom.: 1373 Cov.: 32 AF XY: 0.0717 AC XY: 5330 AN XY: 74360

African (AFR) AF: 0.252 AC: 10433 AN: 41434

American (AMR) AF: 0.0310 AC: 475 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0300 AC: 104 AN: 3466

East Asian (EAS) AF: 0.0215 AC: 111 AN: 5170

South Asian (SAS) AF: 0.00477 AC: 23 AN: 4820

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10612

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.00138 AC: 94 AN: 67994

Other (OTH) AF: 0.0491 AC: 104 AN: 2116

Alfa AF: 0.0696 Hom.: 112

Bravo AF: 0.0848

Asia WGS AF: 0.0220 AC: 77 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	0.30
DANN	Benign	0.45
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2102264; hg19: chr15-78728608;