rs1657265

Positions:

• chr7-155106323-C-T

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: ENST00000622492.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000622492.1	n.78G>A		non_coding_transcript_exon_variant	1/1

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;