ENST00000654974.1:n.1458-13278C>T

Variant names:

• chr1-209160872-G-A
• rs4382726
• ENST00000654974.1:n.1458-13278C>T

Variant summary

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

The ENST00000654974.1(ENSG00000232537):​n.1458-13278C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 151,616 control chromosomes in the GnomAD database, including 27,882 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 0.60 (27882 hom., cov: 32)
• Consequence: ENSG00000232537 ENST00000654974.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.658
• Publications: 5 publications found

Genes affected

ENSG00000232537 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.773 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
ENSG00000232537	ENST00000654974.1	n.1458-13278C>T		intron_variant	Intron 2 of 2
ENSG00000232537	ENST00000660754.1	n.206-13278C>T		intron_variant	Intron 2 of 2
ENSG00000232537	ENST00000661914.2	n.249-7122C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91427 AN: 151498 Hom.: 27864 Cov.: 32

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.603 AC: 91477 AN: 151616 Hom.: 27882 Cov.: 32 AF XY: 0.602 AC XY: 44593 AN XY: 74054

African (AFR) AF: 0.521 AC: 21509 AN: 41290

American (AMR) AF: 0.575 AC: 8770 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2094 AN: 3464

East Asian (EAS) AF: 0.793 AC: 4097 AN: 5168

South Asian (SAS) AF: 0.536 AC: 2575 AN: 4802

European-Finnish (FIN) AF: 0.668 AC: 6957 AN: 10410

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.639 AC: 43405 AN: 67914

Other (OTH) AF: 0.580 AC: 1221 AN: 2106

Alfa AF: 0.522 Hom.: 1475

Bravo AF: 0.596

Asia WGS AF: 0.634 AC: 2205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.42
DANN	Benign	0.48
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs4382726; hg19: chr1-209334217;