rs2115105

Variant names:

• chr16-12614824-G-A
• rs2115105
• ENST00000615100.1:n.374G>A

Variant summary

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

The ENST00000615100.1(ENSG00000274834):​n.374G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,230 control chromosomes in the GnomAD database, including 1,772 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 0.14 (1772 hom., cov: 33)
  • Exomes 𝑓: 0.17 (0 hom.)
• Consequence: ENSG00000274834 ENST00000615100.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

Genes affected

ENSG00000274834 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.279 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
ENSG00000274834	ENST00000615100.1	n.374G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21361 AN: 152088 Hom.: 1774 Cov.: 33

Gnomad AFR AF: 0.0600

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.159

GnomAD4 exome AF: 0.167 AC: 4 AN: 24 Hom.: 0 Cov.: 0 AF XY: 0.222 AC XY: 4 AN XY: 18

Gnomad4 NFE exome AF: 0.182

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.140 AC: 21366 AN: 152206 Hom.: 1772 Cov.: 33 AF XY: 0.139 AC XY: 10353 AN XY: 74388

Gnomad4 AFR AF: 0.0600

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.292

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.160

Alfa AF: 0.168 Hom.: 2951

Bravo AF: 0.130

Asia WGS AF: 0.265 AC: 920 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2115105; hg19: chr16-12708681;