rs12302525

Variant names:

• chr12-89332648-C-G
• rs12302525
• ENST00000765943.1:n.98-4045C>G

Variant summary

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

The ENST00000765943.1(ENSG00000299735):​n.98-4045C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,150 control chromosomes in the GnomAD database, including 1,929 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 0.13 (1929 hom., cov: 31)
• Consequence: ENSG00000299735 ENST00000765943.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.321
• Publications: 3 publications found

Genes affected

ENSG00000299735 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.275 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
ENSG00000299735	ENST00000765943.1	n.98-4045C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19390 AN: 152032 Hom.: 1925 Cov.: 31

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.0396

Gnomad AMR AF: 0.0740

Gnomad ASJ AF: 0.0685

Gnomad EAS AF: 0.00635

Gnomad SAS AF: 0.0757

Gnomad FIN AF: 0.0358

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0797

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.128 AC: 19425 AN: 152150 Hom.: 1929 Cov.: 31 AF XY: 0.122 AC XY: 9111 AN XY: 74382

African (AFR) AF: 0.279 AC: 11581 AN: 41466

American (AMR) AF: 0.0739 AC: 1131 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0685 AC: 237 AN: 3462

East Asian (EAS) AF: 0.00656 AC: 34 AN: 5182

South Asian (SAS) AF: 0.0749 AC: 361 AN: 4818

European-Finnish (FIN) AF: 0.0358 AC: 380 AN: 10600

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0797 AC: 5423 AN: 68008

Other (OTH) AF: 0.108 AC: 227 AN: 2108

Alfa AF: 0.119 Hom.: 177

Bravo AF: 0.136

Asia WGS AF: 0.0570 AC: 200 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.6
DANN	Benign	0.61
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs12302525; hg19: chr12-89726425;