7-155106323-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

ENSG00000274637 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.176 AC: 2016 AN: 11454

American (AMR) AF: 0.185 AC: 6271 AN: 33894

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 2102 AN: 12096

East Asian (EAS) AF: 0.334 AC: 6340 AN: 18988

South Asian (SAS) AF: 0.267 AC: 15010 AN: 56268

European-Finnish (FIN) AF: 0.196 AC: 6490 AN: 33156

Middle Eastern (MID) AF: 0.223 AC: 320 AN: 1434

European-Non Finnish (NFE) AF: 0.230 AC: 49417 AN: 214830

Other (OTH) AF: 0.222 AC: 4338 AN: 19498

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

African (AFR) AF: 0.175 AC: 7256 AN: 41436

American (AMR) AF: 0.207 AC: 3173 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 645 AN: 3470

East Asian (EAS) AF: 0.356 AC: 1841 AN: 5168

South Asian (SAS) AF: 0.261 AC: 1256 AN: 4806

European-Finnish (FIN) AF: 0.208 AC: 2188 AN: 10544

Middle Eastern (MID) AF: 0.188 AC: 55 AN: 292

European-Non Finnish (NFE) AF: 0.241 AC: 16418 AN: 67984

Other (OTH) AF: 0.228 AC: 480 AN: 2102

Alfa AF: 0.233 Hom.: 13015

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
PhyloP100		-0.047

Splicing

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

Other links and lift over

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