rs4275453

Variant names:

• chr1-159738257-C-T
• rs4275453
• ENST00000751816.1:n.245-1832C>T

Variant summary

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

The ENST00000751816.1(ENSG00000297913):​n.245-1832C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 151,950 control chromosomes in the GnomAD database, including 29,285 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 0.61 (29285 hom., cov: 31)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.303
• Publications: 9 publications found

Genes affected

ENSG00000297913 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751816.1. 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
	ENSG00000297913	ENST00000751816.1		n.245-1832C>T		intron	N/A
	ENSG00000297913	ENST00000751817.1		n.357-1505C>T		intron	N/A
	ENSG00000297913	ENST00000751818.1		n.200-1505C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92789 AN: 151834 Hom.: 29258 Cov.: 31

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.753

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.611 AC: 92858 AN: 151950 Hom.: 29285 Cov.: 31 AF XY: 0.617 AC XY: 45820 AN XY: 74290

African (AFR) AF: 0.444 AC: 18402 AN: 41418

American (AMR) AF: 0.706 AC: 10776 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.704 AC: 2442 AN: 3470

East Asian (EAS) AF: 0.684 AC: 3535 AN: 5166

South Asian (SAS) AF: 0.550 AC: 2656 AN: 4830

European-Finnish (FIN) AF: 0.753 AC: 7944 AN: 10556

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.663 AC: 45070 AN: 67940

Other (OTH) AF: 0.619 AC: 1307 AN: 2110

Alfa AF: 0.630 Hom.: 8767

Bravo AF: 0.602

Asia WGS AF: 0.629 AC: 2187 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.86
DANN	Benign	0.18
PhyloP100		-0.30

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: rs4275453;

hg19: chr1-159708047;