7-25831489-C-T

Variant names:

• chr7-25831489-C-T
• rs1055144
• ENST00000666265.2:n.476G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000666265.2(ENSG00000286725):​n.476G>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 0.169 in 152,128 control chromosomes in the GnomAD database, including 2,914 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 0.17 (2914 hom., cov: 32)
• Consequence: ENSG00000286725 ENST00000666265.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.579
• Publications: 86 publications found

Genes affected

ENSG00000286725 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100506236	XR_108752.5	n.430G>A		non_coding_transcript_exon_variant	Exon 3 of 3
LOC100506236	XR_927110.3	n.368G>A		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286725	ENST00000666265.2	n.476G>A		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000286725	ENST00000812200.1	n.389G>A		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000286725	ENST00000812201.1	n.470G>A		non_coding_transcript_exon_variant	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25754 AN: 152010 Hom.: 2914 Cov.: 32

Gnomad AFR AF: 0.0555

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.181

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.169 AC: 25764 AN: 152128 Hom.: 2914 Cov.: 32 AF XY: 0.178 AC XY: 13210 AN XY: 74336

African (AFR) AF: 0.0554 AC: 2302 AN: 41546

American (AMR) AF: 0.157 AC: 2405 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 526 AN: 3472

East Asian (EAS) AF: 0.424 AC: 2188 AN: 5156

South Asian (SAS) AF: 0.426 AC: 2051 AN: 4812

European-Finnish (FIN) AF: 0.265 AC: 2804 AN: 10562

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 12959 AN: 67978

Other (OTH) AF: 0.179 AC: 378 AN: 2108

Alfa AF: 0.186 Hom.: 9773

Bravo AF: 0.151

Asia WGS AF: 0.369 AC: 1281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.30
DANN	Benign	0.60
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs1055144; hg19: chr7-25871109;