3-25875675-T-C

Position:

• chr3-25875675-T-C

Variant summary

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

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.389

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.25875675T>C		intergenic_region
LOC124909357	XR_007095848.1	n.123+1775T>C		intron_variant
LOC124909357	XR_007095849.1	n.226+1672T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.675

Gnomad4 AMR AF: 0.845

Gnomad4 ASJ AF: 0.815

Gnomad4 EAS AF: 0.973

Gnomad4 SAS AF: 0.781

Gnomad4 FIN AF: 0.814

Gnomad4 NFE AF: 0.812

Gnomad4 OTH AF: 0.800

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6793031; hg19: chr3-25917166;