rs2278076

Positions:

• chr15-67807262-G-A

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 0.218 in 206,572 control chromosomes in the GnomAD database, including 6,650 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 (4598 hom., cov: 33)
  • Exomes 𝑓: 0.24 (2052 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.67807262G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32137 AN: 152034 Hom.: 4581 Cov.: 33

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.241

GnomAD4 exome AF: 0.238 AC: 12940 AN: 54418 Hom.: 2052 AF XY: 0.246 AC XY: 7087 AN XY: 28820

Gnomad4 AFR exome AF: 0.100

Gnomad4 AMR exome AF: 0.497

Gnomad4 ASJ exome AF: 0.297

Gnomad4 EAS exome AF: 0.578

Gnomad4 SAS exome AF: 0.303

Gnomad4 FIN exome AF: 0.115

Gnomad4 NFE exome AF: 0.180

Gnomad4 OTH exome AF: 0.210

GnomAD4 genome AF: 0.211 AC: 32167 AN: 152154 Hom.: 4598 Cov.: 33 AF XY: 0.216 AC XY: 16038 AN XY: 74388

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.340

Gnomad4 EAS AF: 0.593

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.244

Alfa AF: 0.209 Hom.: 396

Bravo AF: 0.232

Asia WGS AF: 0.468 AC: 1627 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.6
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2278076; hg19: chr15-68099600;