12-10614592-T-C

Variant names:

• chr12-10614592-T-C
• rs6488313
• ENST00000790608.1:n.258+697T>C

Variant summary

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

The ENST00000790608.1(ENSG00000302947):​n.258+697T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.762 in 152,130 control chromosomes in the GnomAD database, including 44,822 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 0.76 (44822 hom., cov: 32)
• Consequence: ENSG00000302947 ENST00000790608.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.360
• Publications: 4 publications found

Genes affected

ENSG00000302947 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 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
ENSG00000302947	ENST00000790608.1	n.258+697T>C		intron_variant	Intron 1 of 1
ENSG00000302947	ENST00000790609.1	n.239+268T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.762 AC: 115899 AN: 152012 Hom.: 44787 Cov.: 32

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.836

Gnomad FIN AF: 0.818

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.791

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.762 AC: 115988 AN: 152130 Hom.: 44822 Cov.: 32 AF XY: 0.764 AC XY: 56812 AN XY: 74364

African (AFR) AF: 0.638 AC: 26455 AN: 41464

American (AMR) AF: 0.830 AC: 12681 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.740 AC: 2568 AN: 3470

East Asian (EAS) AF: 0.995 AC: 5159 AN: 5184

South Asian (SAS) AF: 0.835 AC: 4028 AN: 4824

European-Finnish (FIN) AF: 0.818 AC: 8648 AN: 10578

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.791 AC: 53800 AN: 68004

Other (OTH) AF: 0.777 AC: 1645 AN: 2116

Alfa AF: 0.774 Hom.: 5687

Bravo AF: 0.760

Asia WGS AF: 0.906 AC: 3150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.6
DANN	Benign	0.80
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs6488313; hg19: chr12-10767191;