1-172682628-T-A

Variant names:

• chr1-172682628-T-A
• rs859654
• ENST00000725727.1:n.69+12029T>A

Variant summary

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

The ENST00000725727.1(ENSG00000224000):​n.69+12029T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 151,968 control chromosomes in the GnomAD database, including 12,025 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 0.38 (12025 hom., cov: 31)
• Consequence: ENSG00000224000 ENST00000725727.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.255
• Publications: 4 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000725727.1. 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
	ENSG00000224000	ENST00000725727.1		n.69+12029T>A		intron	N/A
	ENSG00000224000	ENST00000725728.1		n.108+2926T>A		intron	N/A
	ENSG00000224000	ENST00000725729.1		n.36+2926T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.382 AC: 58067 AN: 151848 Hom.: 12017 Cov.: 31

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.00926

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.382 AC: 58097 AN: 151968 Hom.: 12025 Cov.: 31 AF XY: 0.374 AC XY: 27783 AN XY: 74258

African (AFR) AF: 0.516 AC: 21389 AN: 41412

American (AMR) AF: 0.315 AC: 4806 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1398 AN: 3468

East Asian (EAS) AF: 0.00909 AC: 47 AN: 5170

South Asian (SAS) AF: 0.201 AC: 970 AN: 4828

European-Finnish (FIN) AF: 0.325 AC: 3430 AN: 10546

Middle Eastern (MID) AF: 0.476 AC: 139 AN: 292

European-Non Finnish (NFE) AF: 0.365 AC: 24820 AN: 67966

Other (OTH) AF: 0.370 AC: 781 AN: 2110

Alfa AF: 0.373 Hom.: 1324

Bravo AF: 0.390

Asia WGS AF: 0.131 AC: 458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.9
DANN	Benign	0.73
PhyloP100		0.26

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: rs859654;

hg19: chr1-172651768;