7-25263847-C-T

Variant names:

• chr7-25263847-C-T
• rs2717907
• ENST00000776773.1:n.275+877G>A

Variant summary

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

The ENST00000776773.1(ENSG00000301168):​n.275+877G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.824 in 152,216 control chromosomes in the GnomAD database, including 51,729 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 0.82 (51729 hom., cov: 33)
• Consequence: ENSG00000301168 ENST00000776773.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.214
• Publications: 3 publications found

Genes affected

ENSG00000301168 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.

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
ENSG00000301168	ENST00000776773.1	n.275+877G>A		intron_variant	Intron 3 of 3
ENSG00000301168	ENST00000776774.1	n.445+877G>A		intron_variant	Intron 3 of 3
ENSG00000301168	ENST00000776775.1	n.168-3544G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.824 AC: 125392 AN: 152098 Hom.: 51677 Cov.: 33

Gnomad AFR AF: 0.842

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.892

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.785

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.845

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

GnomAD4 genome AF: 0.824 AC: 125500 AN: 152216 Hom.: 51729 Cov.: 33 AF XY: 0.823 AC XY: 61209 AN XY: 74412

African (AFR) AF: 0.842 AC: 34956 AN: 41532

American (AMR) AF: 0.828 AC: 12656 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.892 AC: 3094 AN: 3470

East Asian (EAS) AF: 0.865 AC: 4484 AN: 5186

South Asian (SAS) AF: 0.785 AC: 3781 AN: 4814

European-Finnish (FIN) AF: 0.760 AC: 8053 AN: 10594

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.818 AC: 55662 AN: 68008

Other (OTH) AF: 0.847 AC: 1792 AN: 2116

Alfa AF: 0.829 Hom.: 150814

Bravo AF: 0.834

Asia WGS AF: 0.808 AC: 2810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.7
DANN	Benign	0.61
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs2717907; hg19: chr7-25303466;