chr1-159744359-T-C

Variant names:

• chr1-159744359-T-C
• rs4285692
• ENST00000751880.1:n.325-1125A>G

Variant summary

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

The ENST00000751880.1(ENSG00000297934):​n.325-1125A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.629 in 152,058 control chromosomes in the GnomAD database, including 31,065 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 0.63 (31065 hom., cov: 32)
• Consequence: ENSG00000297934 ENST00000751880.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.924
• Publications: 6 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.783 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.325-1125A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.628 AC: 95460 AN: 151940 Hom.: 31002 Cov.: 32

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.629 AC: 95588 AN: 152058 Hom.: 31065 Cov.: 32 AF XY: 0.630 AC XY: 46851 AN XY: 74332

African (AFR) AF: 0.790 AC: 32772 AN: 41478

American (AMR) AF: 0.694 AC: 10609 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.582 AC: 2015 AN: 3462

East Asian (EAS) AF: 0.699 AC: 3616 AN: 5170

South Asian (SAS) AF: 0.507 AC: 2443 AN: 4820

European-Finnish (FIN) AF: 0.597 AC: 6313 AN: 10568

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.529 AC: 35925 AN: 67962

Other (OTH) AF: 0.613 AC: 1294 AN: 2112

Alfa AF: 0.561 Hom.: 91792

Bravo AF: 0.647

Asia WGS AF: 0.642 AC: 2236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.52
DANN	Benign	0.55
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs4285692; hg19: chr1-159714149;