rs2157453

Variant names:

• chr1-172894808-G-A
• rs2157453
• ENST00000717051.1:n.127G>A

Variant summary

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

The ENST00000717051.1(ENSG00000224000):​n.127G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 152,026 control chromosomes in the GnomAD database, including 9,355 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 0.32 (9355 hom., cov: 32)
• Consequence: ENSG00000224000 ENST00000717051.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231
• Publications: 15 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000717051.1. 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	ENST00000717051.1		n.127G>A		non_coding_transcript_exon	Exon 1 of 4
	ENSG00000224000	ENST00000432694.2	TSL:3	n.224-109474G>A		intron	N/A
	ENSG00000224000	ENST00000717047.1		n.354-5158G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49153 AN: 151908 Hom.: 9351 Cov.: 32

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.896

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.323 AC: 49173 AN: 152026 Hom.: 9355 Cov.: 32 AF XY: 0.332 AC XY: 24673 AN XY: 74300

African (AFR) AF: 0.342 AC: 14184 AN: 41450

American (AMR) AF: 0.466 AC: 7111 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 908 AN: 3462

East Asian (EAS) AF: 0.895 AC: 4626 AN: 5166

South Asian (SAS) AF: 0.418 AC: 2012 AN: 4818

European-Finnish (FIN) AF: 0.296 AC: 3124 AN: 10562

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16278 AN: 67974

Other (OTH) AF: 0.327 AC: 691 AN: 2114

Alfa AF: 0.276 Hom.: 12164

Bravo AF: 0.347

Asia WGS AF: 0.561 AC: 1950 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.9
DANN	Benign	0.40
PhyloP100		0.23

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: rs2157453;

hg19: chr1-172863948;