ENST00000751880.1:n.325-9032G>A

Variant names:

• chr1-159752266-C-T
• rs4131568
• ENST00000751880.1:n.325-9032G>A

Variant summary

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

The ENST00000751880.1(ENSG00000297934):​n.325-9032G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,052 control chromosomes in the GnomAD database, including 6,741 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 (6741 hom., cov: 32)
• Consequence: ENSG00000297934 ENST00000751880.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.183
• Publications: 11 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.343 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.325-9032G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40229 AN: 151934 Hom.: 6738 Cov.: 32

Gnomad AFR AF: 0.0701

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.0557

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.265 AC: 40245 AN: 152052 Hom.: 6741 Cov.: 32 AF XY: 0.272 AC XY: 20178 AN XY: 74314

African (AFR) AF: 0.0699 AC: 2904 AN: 41524

American (AMR) AF: 0.337 AC: 5150 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1071 AN: 3470

East Asian (EAS) AF: 0.0558 AC: 289 AN: 5176

South Asian (SAS) AF: 0.293 AC: 1413 AN: 4824

European-Finnish (FIN) AF: 0.462 AC: 4862 AN: 10534

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23585 AN: 67932

Other (OTH) AF: 0.269 AC: 568 AN: 2112

Alfa AF: 0.313 Hom.: 5874

Bravo AF: 0.249

Asia WGS AF: 0.183 AC: 638 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	0.56
DANN	Benign	0.50
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs4131568; hg19: chr1-159722056;