chr5-6402485-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

ENSG00000287031 (HGNC:58998):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653641.1. 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
	ENSG00000287031	ENST00000653641.1		n.780+2297C>T		intron	N/A
	ENSG00000287031	ENST00000807649.1		n.252-6715C>T		intron	N/A

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

African (AFR) AF: 0.132 AC: 5459 AN: 41504

American (AMR) AF: 0.159 AC: 2429 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0643 AC: 223 AN: 3470

East Asian (EAS) AF: 0.163 AC: 843 AN: 5174

South Asian (SAS) AF: 0.226 AC: 1090 AN: 4826

European-Finnish (FIN) AF: 0.0768 AC: 814 AN: 10596

Middle Eastern (MID) AF: 0.0959 AC: 28 AN: 292

European-Non Finnish (NFE) AF: 0.0470 AC: 3196 AN: 68008

Other (OTH) AF: 0.0830 AC: 175 AN: 2108

Alfa AF: 0.0642 Hom.: 794

Bravo AF: 0.100

Asia WGS AF: 0.172 AC: 598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.7
DANN	Benign	0.24
PhyloP100		0.33

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1393067;

hg19: chr5-6402598;