5-6402485-C-T

Variant names:

• chr5-6402485-C-T
• rs1393067
• ENST00000653641.1:n.780+2297C>T

Variant summary

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

The ENST00000653641.1(ENSG00000287031):​n.780+2297C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0937 in 152,172 control chromosomes in the GnomAD database, including 916 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 0.094 (916 hom., cov: 33)
• Consequence: ENSG00000287031 ENST00000653641.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.334

Genes affected

ENSG00000287031 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.215 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
ENSG00000287031	ENST00000653641.1	n.780+2297C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0937 AC: 14250 AN: 152054 Hom.: 910 Cov.: 33

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.0643

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.0768

Gnomad MID AF: 0.0987

Gnomad NFE AF: 0.0470

Gnomad OTH AF: 0.0810

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

GnomAD4 genome AF: 0.0937 AC: 14263 AN: 152172 Hom.: 916 Cov.: 33 AF XY: 0.0977 AC XY: 7271 AN XY: 74416

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.0643

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.0768

Gnomad4 NFE AF: 0.0470

Gnomad4 OTH AF: 0.0830

Alfa AF: 0.0600 Hom.: 569

Bravo AF: 0.100

Asia WGS AF: 0.172 AC: 598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.7
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1393067; hg19: chr5-6402598;