12-25335097-G-C

Variant names:

• chr12-25335097-G-C
• rs7953098
• ENST00000834589.1:n.256-3316G>C

Variant summary

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

The ENST00000834589.1(ENSG00000308495):​n.256-3316G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 151,764 control chromosomes in the GnomAD database, including 16,494 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 0.45 (16494 hom., cov: 32)
• Consequence: ENSG00000308495 ENST00000834589.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.349
• Publications: 5 publications found

Genes affected

ENSG00000308495 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000834589.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308495	ENST00000834589.1		n.256-3316G>C		intron	N/A
	ENSG00000308495	ENST00000834590.1		n.256-551G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68103 AN: 151646 Hom.: 16490 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.515

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.449 AC: 68128 AN: 151764 Hom.: 16494 Cov.: 32 AF XY: 0.447 AC XY: 33134 AN XY: 74164

African (AFR) AF: 0.266 AC: 11004 AN: 41340

American (AMR) AF: 0.393 AC: 5998 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2328 AN: 3470

East Asian (EAS) AF: 0.515 AC: 2665 AN: 5170

South Asian (SAS) AF: 0.511 AC: 2462 AN: 4816

European-Finnish (FIN) AF: 0.488 AC: 5125 AN: 10500

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.543 AC: 36868 AN: 67904

Other (OTH) AF: 0.465 AC: 983 AN: 2112

Alfa AF: 0.342 Hom.: 946

Bravo AF: 0.432

Asia WGS AF: 0.452 AC: 1566 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	13
DANN	Benign	0.62
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs7953098; hg19: chr12-25488031;