7-25946953-G-A

Variant names:

• chr7-25946953-G-A
• rs4719839
• ENST00000718758.1:n.605-7492C>T

Variant summary

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

The ENST00000718758.1(ENSG00000293754):​n.605-7492C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.751 in 152,172 control chromosomes in the GnomAD database, including 43,623 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 0.75 (43623 hom., cov: 32)
• Consequence: ENSG00000293754 ENST00000718758.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800
• Publications: 4 publications found

Genes affected

ENSG00000293754 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000718758.1. 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
	ENSG00000293754	ENST00000718758.1		n.605-7492C>T		intron	N/A
	ENSG00000293754	ENST00000718759.1		n.871+5012C>T		intron	N/A
	ENSG00000293754	ENST00000718760.1		n.665-7492C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.751 AC: 114159 AN: 152056 Hom.: 43574 Cov.: 32

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.751 AC: 114268 AN: 152172 Hom.: 43623 Cov.: 32 AF XY: 0.750 AC XY: 55785 AN XY: 74382

African (AFR) AF: 0.889 AC: 36959 AN: 41552

American (AMR) AF: 0.743 AC: 11345 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.714 AC: 2478 AN: 3470

East Asian (EAS) AF: 0.616 AC: 3192 AN: 5182

South Asian (SAS) AF: 0.658 AC: 3168 AN: 4818

European-Finnish (FIN) AF: 0.714 AC: 7542 AN: 10566

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.695 AC: 47267 AN: 67992

Other (OTH) AF: 0.748 AC: 1578 AN: 2110

Alfa AF: 0.684 Hom.: 2553

Bravo AF: 0.760

Asia WGS AF: 0.664 AC: 2308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.78
DANN	Benign	0.20
PhyloP100		-0.0080

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: rs4719839;

hg19: chr7-25986573;