7-25375447-A-T

Position:

• chr7-25375447-A-T

Variant summary

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

The ENST00000669800.1(ENSG00000260951):​n.280-15601T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 152,194 control chromosomes in the GnomAD database, including 3,882 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 0.20 (3882 hom., cov: 32)
• Consequence: ENSG00000260951 ENST00000669800.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.756

Genes affected

ENSG00000260951 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901604	XR_007060262.1	n.128+3854T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000260951	ENST00000669800.1	n.280-15601T>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.204 AC: 30995 AN: 152076 Hom.: 3885 Cov.: 32

Gnomad AFR AF: 0.0936

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.0285

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.204 AC: 30982 AN: 152194 Hom.: 3882 Cov.: 32 AF XY: 0.201 AC XY: 14960 AN XY: 74416

Gnomad4 AFR AF: 0.0934

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.0285

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.201

Alfa AF: 0.150 Hom.: 317

Bravo AF: 0.187

Asia WGS AF: 0.0850 AC: 296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.3
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2188993; hg19: chr7-25415066;