rs598714

Variant names:

• chr1-181857793-C-A
• rs598714
• ENST00000717053.1:n.288-22157G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-181857793-C-A
• chr1-181857793-C-G

Variant summary

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

The ENST00000717053.1(ENSG00000287452):​n.288-22157G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.702 in 151,972 control chromosomes in the GnomAD database, including 37,604 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 0.70 (37604 hom., cov: 31)
• Consequence: ENSG00000287452 ENST00000717053.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0960
• Publications: 1 publications found

Genes affected

ENSG00000287452 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000717053.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287452	ENST00000717053.1		n.288-22157G>T		intron	N/A
	ENSG00000287452	ENST00000717054.1		n.293-22157G>T		intron	N/A
	ENSG00000287452	ENST00000717055.1		n.81-22157G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.702 AC: 106594 AN: 151854 Hom.: 37581 Cov.: 31

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.692

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.702 AC: 106662 AN: 151972 Hom.: 37604 Cov.: 31 AF XY: 0.699 AC XY: 51900 AN XY: 74286

African (AFR) AF: 0.737 AC: 30535 AN: 41452

American (AMR) AF: 0.708 AC: 10797 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2118 AN: 3472

East Asian (EAS) AF: 0.563 AC: 2901 AN: 5154

South Asian (SAS) AF: 0.692 AC: 3337 AN: 4822

European-Finnish (FIN) AF: 0.714 AC: 7539 AN: 10556

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.692 AC: 47044 AN: 67948

Other (OTH) AF: 0.708 AC: 1491 AN: 2106

Alfa AF: 0.686 Hom.: 53961

Bravo AF: 0.702

Asia WGS AF: 0.629 AC: 2190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.37
PhyloP100		0.096

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs598714;

hg19: chr1-181826928;