7-155106368-T-C

Position:

• chr7-155106368-T-C

Variant summary

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

The ENST00000622492.1(ENSG00000274637):​n.33A>G 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 0.726 in 453,572 control chromosomes in the GnomAD database, including 120,080 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 0.69 (36713 hom., cov: 32)
  • Exomes 𝑓: 0.74 (83367 hom.)
• Consequence: ENSG00000274637 ENST00000622492.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.334

Genes affected

ENSG00000274637 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.771 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.155106368T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000274637	ENST00000622492.1	n.33A>G		non_coding_transcript_exon_variant	1/1	6
ENSG00000228806	ENST00000436250.1	n.-32T>C		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.694 AC: 105428 AN: 151874 Hom.: 36686 Cov.: 32

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.791

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.687

GnomAD4 exome AF: 0.743 AC: 223949 AN: 301580 Hom.: 83367 Cov.: 2 AF XY: 0.742 AC XY: 123002 AN XY: 165708

Gnomad4 AFR exome AF: 0.769

Gnomad4 AMR exome AF: 0.824

Gnomad4 ASJ exome AF: 0.765

Gnomad4 EAS exome AF: 0.852

Gnomad4 SAS exome AF: 0.759

Gnomad4 FIN exome AF: 0.633

Gnomad4 NFE exome AF: 0.734

Gnomad4 OTH exome AF: 0.731

GnomAD4 genome AF: 0.694 AC: 105501 AN: 151992 Hom.: 36713 Cov.: 32 AF XY: 0.695 AC XY: 51615 AN XY: 74308

Gnomad4 AFR AF: 0.714

Gnomad4 AMR AF: 0.741

Gnomad4 ASJ AF: 0.705

Gnomad4 EAS AF: 0.791

Gnomad4 SAS AF: 0.695

Gnomad4 FIN AF: 0.607

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.683

Alfa AF: 0.683 Hom.: 37254

Bravo AF: 0.705

Asia WGS AF: 0.685 AC: 2382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.64
DANN	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1619015; hg19: chr7-154898078; COSMIC: COSV71452477;