rs12778642

Variant names:

• chr10-92704550-G-T
• rs12778642
• ENST00000788997.1:n.152-1699G>T

Variant summary

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

The ENST00000788997.1(ENSG00000302698):​n.152-1699G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 151,846 control chromosomes in the GnomAD database, including 15,608 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 (15608 hom., cov: 31)
• Consequence: ENSG00000302698 ENST00000788997.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 31 publications found

Genes affected

ENSG00000302698 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.738 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
ENSG00000302698	ENST00000788997.1	n.152-1699G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.448 AC: 67969 AN: 151728 Hom.: 15601 Cov.: 31

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.448 AC: 68013 AN: 151846 Hom.: 15608 Cov.: 31 AF XY: 0.451 AC XY: 33430 AN XY: 74196

African (AFR) AF: 0.427 AC: 17662 AN: 41388

American (AMR) AF: 0.410 AC: 6251 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1308 AN: 3470

East Asian (EAS) AF: 0.758 AC: 3888 AN: 5132

South Asian (SAS) AF: 0.587 AC: 2821 AN: 4806

European-Finnish (FIN) AF: 0.481 AC: 5070 AN: 10550

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29405 AN: 67924

Other (OTH) AF: 0.433 AC: 913 AN: 2110

Alfa AF: 0.432 Hom.: 27972

Bravo AF: 0.440

Asia WGS AF: 0.619 AC: 2151 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	0.76
DANN	Benign	0.39
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs12778642; hg19: chr10-94464307;