1-159703795-G-A

Variant names:

• chr1-159703795-G-A
• rs1572970
• ENST00000751816.1:n.108-22732G>A

Variant summary

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

The ENST00000751816.1(ENSG00000297913):​n.108-22732G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.612 in 151,974 control chromosomes in the GnomAD database, including 30,582 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 0.61 (30582 hom., cov: 31)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.824
• Publications: 14 publications found

Genes affected

ENSG00000297913 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751816.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297913	ENST00000751816.1		n.108-22732G>A		intron	N/A
	ENSG00000297913	ENST00000751817.1		n.110-22732G>A		intron	N/A
	ENSG00000297913	ENST00000751818.1		n.63-22732G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.612 AC: 92991 AN: 151856 Hom.: 30568 Cov.: 31

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.661

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.612 AC: 93033 AN: 151974 Hom.: 30582 Cov.: 31 AF XY: 0.616 AC XY: 45777 AN XY: 74308

African (AFR) AF: 0.351 AC: 14519 AN: 41422

American (AMR) AF: 0.737 AC: 11260 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2459 AN: 3468

East Asian (EAS) AF: 0.660 AC: 3413 AN: 5168

South Asian (SAS) AF: 0.593 AC: 2856 AN: 4818

European-Finnish (FIN) AF: 0.749 AC: 7924 AN: 10582

Middle Eastern (MID) AF: 0.596 AC: 174 AN: 292

European-Non Finnish (NFE) AF: 0.711 AC: 48329 AN: 67928

Other (OTH) AF: 0.638 AC: 1350 AN: 2116

Alfa AF: 0.684 Hom.: 60810

Bravo AF: 0.602

Asia WGS AF: 0.618 AC: 2152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.45
DANN	Benign	0.58
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs1572970; hg19: chr1-159673585;