1-172741860-T-C

Variant names:

• chr1-172741860-T-C
• rs859637
• ENST00000725727.1:n.70-33959T>C

Variant summary

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

The ENST00000725727.1(ENSG00000224000):​n.70-33959T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.557 in 151,986 control chromosomes in the GnomAD database, including 25,115 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 0.56 (25115 hom., cov: 31)
• Consequence: ENSG00000224000 ENST00000725727.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.711
• Publications: 17 publications found

Genes affected

ENSG00000224000 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.724 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
ENSG00000224000	ENST00000725727.1	n.70-33959T>C		intron_variant	Intron 1 of 1
ENSG00000224000	ENST00000725728.1	n.109-33959T>C		intron_variant	Intron 1 of 1
ENSG00000224000	ENST00000725729.1	n.60+1624T>C		intron_variant	Intron 2 of 2
ENSG00000224000	ENST00000725730.1	n.63+1624T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84521 AN: 151868 Hom.: 25072 Cov.: 31

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.0786

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.557 AC: 84619 AN: 151986 Hom.: 25115 Cov.: 31 AF XY: 0.548 AC XY: 40707 AN XY: 74316

African (AFR) AF: 0.731 AC: 30314 AN: 41448

American (AMR) AF: 0.445 AC: 6796 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2146 AN: 3470

East Asian (EAS) AF: 0.0788 AC: 408 AN: 5180

South Asian (SAS) AF: 0.562 AC: 2702 AN: 4808

European-Finnish (FIN) AF: 0.429 AC: 4525 AN: 10560

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.528 AC: 35884 AN: 67940

Other (OTH) AF: 0.550 AC: 1160 AN: 2108

Alfa AF: 0.533 Hom.: 37470

Bravo AF: 0.559

Asia WGS AF: 0.393 AC: 1373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.45
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs859637; hg19: chr1-172711000;