rs1657265

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr7-155106323-C-A
• chr7-155106323-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000622492.1(ENSG00000274637):​n.78G>T 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 0.00000248 in 403,394 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000025 (0 hom.)
• Consequence: ENSG00000274637 ENST00000622492.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470
• Publications: 0 publications found

Genes affected

ENSG00000274637 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).

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>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000228806	ENST00000436250.1	n.-77C>A		upstream_gene_variant		6

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000248 AC: 1 AN: 403394 Hom.: 0 Cov.: 2 AF XY: 0.00 AC XY: 0 AN XY: 225060

African (AFR) AF: 0.00 AC: 0 AN: 11514

American (AMR) AF: 0.00 AC: 0 AN: 33988

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12142

East Asian (EAS) AF: 0.00 AC: 0 AN: 19120

South Asian (SAS) AF: 0.00 AC: 0 AN: 56402

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 33270

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1440

European-Non Finnish (NFE) AF: 0.00000463 AC: 1 AN: 215930

Other (OTH) AF: 0.00 AC: 0 AN: 19588

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	0.80
DANN	Benign	0.49
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;