1-247184887-C-T

Position:

• chr1-247184887-C-T

Variant summary

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

The ENST00000400933.2(ENSG00000215795):​n.596G>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 0.169 in 589,398 control chromosomes in the GnomAD database, including 10,531 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 (1717 hom., cov: 32)
  • Exomes 𝑓: 0.18 (8814 hom.)
• Consequence: ENSG00000215795 ENST00000400933.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.312

Genes affected

ENSG00000215795 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100131465		n.247184887C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000215795	ENST00000400933.2	n.596G>A		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20052 AN: 152098 Hom.: 1716 Cov.: 32

Gnomad AFR AF: 0.0319

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.145

GnomAD4 exome AF: 0.183 AC: 79787 AN: 437182 Hom.: 8814 Cov.: 0 AF XY: 0.197 AC XY: 47813 AN XY: 243088

Gnomad4 AFR exome AF: 0.0293

Gnomad4 AMR exome AF: 0.107

Gnomad4 ASJ exome AF: 0.187

Gnomad4 EAS exome AF: 0.220

Gnomad4 SAS exome AF: 0.338

Gnomad4 FIN exome AF: 0.162

Gnomad4 NFE exome AF: 0.162

Gnomad4 OTH exome AF: 0.161

GnomAD4 genome AF: 0.132 AC: 20052 AN: 152216 Hom.: 1717 Cov.: 32 AF XY: 0.136 AC XY: 10104 AN XY: 74404

Gnomad4 AFR AF: 0.0318

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.174

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.143

Alfa AF: 0.154 Hom.: 841

Bravo AF: 0.122

Asia WGS AF: 0.203 AC: 707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	3.3
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3738443; hg19: chr1-247348189; COSMIC: COSV68931107;