7-155106323-C-T

Variant names:

• chr7-155106323-C-T
• rs1657265
• ENST00000622492.1:n.78G>A

Variant summary

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

The ENST00000622492.1(ENSG00000274637):​n.78G>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 0.227 in 553,620 control chromosomes in the GnomAD database, including 15,131 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 0.22 (3852 hom., cov: 32)
  • Exomes 𝑓: 0.23 (11279 hom.)
• Consequence: ENSG00000274637 ENST00000622492.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470

Genes affected

ENSG00000274637 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.343 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
ENSG00000274637	ENST00000622492.1	n.78G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000228806	ENST00000436250.1	n.-77C>T		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33562 AN: 151884 Hom.: 3848 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.229

GnomAD4 exome AF: 0.230 AC: 92304 AN: 401618 Hom.: 11279 Cov.: 2 AF XY: 0.234 AC XY: 52366 AN XY: 224116

Gnomad4 AFR exome AF: 0.176

Gnomad4 AMR exome AF: 0.185

Gnomad4 ASJ exome AF: 0.174

Gnomad4 EAS exome AF: 0.334

Gnomad4 SAS exome AF: 0.267

Gnomad4 FIN exome AF: 0.196

Gnomad4 NFE exome AF: 0.230

Gnomad4 OTH exome AF: 0.222

GnomAD4 genome AF: 0.221 AC: 33584 AN: 152002 Hom.: 3852 Cov.: 32 AF XY: 0.220 AC XY: 16366 AN XY: 74294

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.356

Gnomad4 SAS AF: 0.261

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.228

Alfa AF: 0.233 Hom.: 4368

Bravo AF: 0.221

Asia WGS AF: 0.270 AC: 938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	2.5
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1657265; hg19: chr7-154898033; COSMIC: COSV71452444;