rs4673364

Variant names:

• chr2-206868387-C-T
• rs4673364
• ENST00000658889.1:n.2974-10996C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000658889.1(ENSG00000229321):​n.2974-10996C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,118 control chromosomes in the GnomAD database, including 1,015 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 0.11 (1015 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000229321 ENST00000658889.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.03

Genes affected

ENSG00000229321 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.196 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
ENSG00000229321	ENST00000658889.1	n.2974-10996C>T		intron_variant	Intron 1 of 4
ENSG00000229321	ENST00000438070.2	n.*98C>T		downstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16727 AN: 152000 Hom.: 1012 Cov.: 32

Gnomad AFR AF: 0.0728

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.0820

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.110 AC: 16729 AN: 152118 Hom.: 1015 Cov.: 32 AF XY: 0.112 AC XY: 8299 AN XY: 74358

Gnomad4 AFR AF: 0.0725

Gnomad4 AMR AF: 0.0820

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.105

Alfa AF: 0.117 Hom.: 2270

Bravo AF: 0.104

Asia WGS AF: 0.206 AC: 717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.013
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4673364; hg19: chr2-207733111;