rs724767

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000238043 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000238043	ENST00000426616.1	n.330-1321C>T		intron_variant	Intron 2 of 2	4

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

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.119

Alfa AF: 0.110 Hom.: 1369

Bravo AF: 0.139

Asia WGS AF: 0.162 AC: 562 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs724767; hg19: chr3-193722330;