7-25375447-A-T

Variant names:

• chr7-25375447-A-T
• rs2188993
• ENST00000669800.2:n.295-15601T>A

Variant summary

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

The ENST00000669800.2(ENSG00000233824):​n.295-15601T>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: ENSG00000233824 ENST00000669800.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.756
• Publications: 3 publications found

Genes affected

ENSG00000233824 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000669800.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000233824	ENST00000669800.2		n.295-15601T>A		intron	N/A
	ENSG00000233824	ENST00000718235.1		n.283-30354T>A		intron	N/A
	ENSG00000233824	ENST00000765804.1		n.265-30354T>A		intron	N/A

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

African (AFR) AF: 0.0934 AC: 3879 AN: 41544

American (AMR) AF: 0.150 AC: 2295 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 804 AN: 3468

East Asian (EAS) AF: 0.0285 AC: 148 AN: 5184

South Asian (SAS) AF: 0.131 AC: 633 AN: 4828

European-Finnish (FIN) AF: 0.306 AC: 3242 AN: 10578

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.283 AC: 19265 AN: 67980

Other (OTH) AF: 0.201 AC: 424 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.3
DANN	Benign	0.87
PhyloP100		0.76

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2188993;

hg19: chr7-25415066;