7-155106368-T-C

Variant names:

• chr7-155106368-T-C
• rs1619015
• ENST00000622492.1:n.33A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 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=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.771 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000622492.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000274637	ENST00000622492.1	TSL:6	n.33A>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000228806	ENST00000436250.1	TSL:6	n.-32T>C		upstream_gene	N/A

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

African (AFR) AF: 0.769 AC: 6713 AN: 8728

American (AMR) AF: 0.824 AC: 19870 AN: 24110

Ashkenazi Jewish (ASJ) AF: 0.765 AC: 6085 AN: 7958

East Asian (EAS) AF: 0.852 AC: 13511 AN: 15854

South Asian (SAS) AF: 0.759 AC: 29230 AN: 38504

European-Finnish (FIN) AF: 0.633 AC: 18033 AN: 28482

Middle Eastern (MID) AF: 0.751 AC: 757 AN: 1008

European-Non Finnish (NFE) AF: 0.734 AC: 118730 AN: 161856

Other (OTH) AF: 0.731 AC: 11020 AN: 15080

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

African (AFR) AF: 0.714 AC: 29611 AN: 41454

American (AMR) AF: 0.741 AC: 11326 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.705 AC: 2446 AN: 3470

East Asian (EAS) AF: 0.791 AC: 4092 AN: 5172

South Asian (SAS) AF: 0.695 AC: 3339 AN: 4806

European-Finnish (FIN) AF: 0.607 AC: 6401 AN: 10546

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.678 AC: 46076 AN: 67958

Other (OTH) AF: 0.683 AC: 1436 AN: 2104

Alfa AF: 0.686 Hom.: 48375

Bravo AF: 0.705

Asia WGS AF: 0.685 AC: 2382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.64
DANN	Benign	0.12
PhyloP100		-0.33

Splicing

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

Other links and lift over

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