12-96044863-G-T

Variant names:

• chr12-96044863-G-T
• rs7966098
• ENST00000824362.1:n.272-2755G>T

Variant summary

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

The ENST00000824362.1(ENSG00000307169):​n.272-2755G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.558 in 151,882 control chromosomes in the GnomAD database, including 23,997 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 0.56 (23997 hom., cov: 30)
• Consequence: ENSG00000307169 ENST00000824362.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358
• Publications: 7 publications found

Genes affected

ENSG00000307169 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.609 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
ENSG00000307169	ENST00000824362.1	n.272-2755G>T		intron_variant	Intron 1 of 2
ENSG00000307169	ENST00000824363.1	n.98-8481G>T		intron_variant	Intron 1 of 1
ENSG00000307169	ENST00000824364.1	n.143-2755G>T		intron_variant	Intron 1 of 2
ENSG00000307169	ENST00000824365.1	n.*138G>T		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84759 AN: 151764 Hom.: 23976 Cov.: 30

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.558 AC: 84820 AN: 151882 Hom.: 23997 Cov.: 30 AF XY: 0.562 AC XY: 41748 AN XY: 74230

African (AFR) AF: 0.615 AC: 25468 AN: 41410

American (AMR) AF: 0.437 AC: 6681 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.482 AC: 1673 AN: 3468

East Asian (EAS) AF: 0.423 AC: 2165 AN: 5120

South Asian (SAS) AF: 0.561 AC: 2699 AN: 4812

European-Finnish (FIN) AF: 0.700 AC: 7394 AN: 10566

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.544 AC: 36961 AN: 67920

Other (OTH) AF: 0.552 AC: 1164 AN: 2110

Alfa AF: 0.538 Hom.: 26602

Bravo AF: 0.539

Asia WGS AF: 0.518 AC: 1801 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.62
DANN	Benign	0.79
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs7966098; hg19: chr12-96438641;