rs724767

Variant names:

• chr3-194004541-C-T
• rs724767
• ENST00000426616.1:n.330-1321C>T

Variant summary

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

The ENST00000426616.1(ENSG00000238043):​n.330-1321C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,150 control chromosomes in the GnomAD database, including 1,466 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 0.13 (1466 hom., cov: 32)
• Consequence: ENSG00000238043 ENST00000426616.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0810
• Publications: 15 publications found

Genes affected

ENSG00000238043 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000426616.1. 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
	ENSG00000238043	ENST00000426616.1	TSL:4	n.330-1321C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20194 AN: 152030 Hom.: 1457 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.0989

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.133 AC: 20233 AN: 152150 Hom.: 1466 Cov.: 32 AF XY: 0.133 AC XY: 9917 AN XY: 74388

African (AFR) AF: 0.183 AC: 7573 AN: 41480

American (AMR) AF: 0.147 AC: 2243 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 422 AN: 3472

East Asian (EAS) AF: 0.156 AC: 805 AN: 5172

South Asian (SAS) AF: 0.138 AC: 666 AN: 4826

European-Finnish (FIN) AF: 0.122 AC: 1295 AN: 10588

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6850 AN: 68018

Other (OTH) AF: 0.119 AC: 252 AN: 2110

Alfa AF: 0.118 Hom.: 2280

Bravo AF: 0.139

Asia WGS AF: 0.162 AC: 562 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.5
DANN	Benign	0.61
PhyloP100		-0.081

Splicing

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

Other links and lift over

dbSNP: rs724767; hg19: chr3-193722330;