3-25875675-T-C

Variant names:

• chr3-25875675-T-C
• rs6793031
• ENST00000829679.1:n.276+1672T>C

Variant summary

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

The ENST00000829679.1(ENSG00000307904):​n.276+1672T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.782 in 152,024 control chromosomes in the GnomAD database, including 46,981 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 0.78 (46981 hom., cov: 31)
• Consequence: ENSG00000307904 ENST00000829679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.389
• Publications: 1 publications found

Genes affected

ENSG00000307904 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124909357	XR_007095848.1	n.123+1775T>C		intron_variant	Intron 1 of 1
LOC124909357	XR_007095849.1	n.226+1672T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307904	ENST00000829679.1	n.276+1672T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.782 AC: 118836 AN: 151906 Hom.: 46943 Cov.: 31

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.752

Gnomad AMR AF: 0.845

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.972

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.812

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.782 AC: 118924 AN: 152024 Hom.: 46981 Cov.: 31 AF XY: 0.785 AC XY: 58389 AN XY: 74342

African (AFR) AF: 0.675 AC: 27957 AN: 41410

American (AMR) AF: 0.845 AC: 12916 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.815 AC: 2829 AN: 3470

East Asian (EAS) AF: 0.973 AC: 5036 AN: 5178

South Asian (SAS) AF: 0.781 AC: 3765 AN: 4820

European-Finnish (FIN) AF: 0.814 AC: 8617 AN: 10588

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.812 AC: 55171 AN: 67958

Other (OTH) AF: 0.800 AC: 1688 AN: 2110

Alfa AF: 0.790 Hom.: 10876

Bravo AF: 0.780

Asia WGS AF: 0.830 AC: 2885 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.54
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs6793031; hg19: chr3-25917166;