1-159744245-C-T

Variant names:

• chr1-159744245-C-T
• rs12760041
• ENST00000751880.1:n.325-1011G>A

Variant summary

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

The ENST00000751880.1(ENSG00000297934):​n.325-1011G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 151,912 control chromosomes in the GnomAD database, including 6,524 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 0.26 (6524 hom., cov: 32)
• Consequence: ENSG00000297934 ENST00000751880.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.345
• Publications: 4 publications found

Genes affected

ENSG00000297934 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.338 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
ENSG00000297934	ENST00000751880.1	n.325-1011G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39595 AN: 151794 Hom.: 6523 Cov.: 32

Gnomad AFR AF: 0.0686

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.0588

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.261 AC: 39609 AN: 151912 Hom.: 6524 Cov.: 32 AF XY: 0.267 AC XY: 19841 AN XY: 74230

African (AFR) AF: 0.0684 AC: 2836 AN: 41440

American (AMR) AF: 0.332 AC: 5071 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1057 AN: 3472

East Asian (EAS) AF: 0.0587 AC: 303 AN: 5162

South Asian (SAS) AF: 0.282 AC: 1359 AN: 4816

European-Finnish (FIN) AF: 0.459 AC: 4830 AN: 10530

Middle Eastern (MID) AF: 0.229 AC: 67 AN: 292

European-Non Finnish (NFE) AF: 0.342 AC: 23204 AN: 67922

Other (OTH) AF: 0.266 AC: 559 AN: 2104

Alfa AF: 0.267 Hom.: 1481

Bravo AF: 0.244

Asia WGS AF: 0.174 AC: 608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.66
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs12760041; hg19: chr1-159714035;