1-160735829-T-C

Variant names:

• chr1-160735829-T-C
• rs549471
• ENST00000792523.1:n.73-3212A>G

Variant summary

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

The ENST00000792523.1(ENSG00000303180):​n.73-3212A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.809 in 144,856 control chromosomes in the GnomAD database, including 47,771 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 0.81 (47771 hom., cov: 23)
• Consequence: ENSG00000303180 ENST00000792523.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 6 publications found

Genes affected

ENSG00000303180 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.969 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000792523.1. 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
	ENSG00000303180	ENST00000792523.1		n.73-3212A>G		intron	N/A
	ENSG00000303180	ENST00000792524.1		n.393-3212A>G		intron	N/A
	ENSG00000303180	ENST00000792525.1		n.658-3212A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.809 AC: 117097 AN: 144736 Hom.: 47733 Cov.: 23

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.834

Gnomad ASJ AF: 0.839

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.925

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.822

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

GnomAD4 genome AF: 0.809 AC: 117192 AN: 144856 Hom.: 47771 Cov.: 23 AF XY: 0.809 AC XY: 56330 AN XY: 69590

African (AFR) AF: 0.739 AC: 29268 AN: 39608

American (AMR) AF: 0.834 AC: 11673 AN: 13990

Ashkenazi Jewish (ASJ) AF: 0.839 AC: 2882 AN: 3434

East Asian (EAS) AF: 0.993 AC: 4701 AN: 4734

South Asian (SAS) AF: 0.925 AC: 4280 AN: 4626

European-Finnish (FIN) AF: 0.772 AC: 6247 AN: 8094

Middle Eastern (MID) AF: 0.830 AC: 239 AN: 288

European-Non Finnish (NFE) AF: 0.826 AC: 55483 AN: 67156

Other (OTH) AF: 0.822 AC: 1668 AN: 2030

Alfa AF: 0.821 Hom.: 94221

Bravo AF: 0.813

Asia WGS AF: 0.929 AC: 3233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.56
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs549471; hg19: chr1-160705619;