rs2115105

chr16-12614824-G-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: ENST00000615100.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000615100.1	n.374G>A		non_coding_transcript_exon_variant	1/1

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;