5-40467170-T-C

Variant names:

• chr5-40467170-T-C
• rs4532399
• ENST00000649444.1:n.119+3490T>C

Variant summary

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

The ENST00000649444.1(ENSG00000285552):​n.119+3490T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 151,792 control chromosomes in the GnomAD database, including 29,153 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 0.61 (29153 hom., cov: 32)
• Consequence: ENSG00000285552 ENST00000649444.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.798
• Publications: 6 publications found

Genes affected

ENSG00000285552 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649444.1. 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
	ENSG00000285552	ENST00000649444.1		n.119+3490T>C		intron	N/A
	ENSG00000285552	ENST00000649894.1		n.119+3490T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93021 AN: 151674 Hom.: 29118 Cov.: 32

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.613 AC: 93114 AN: 151792 Hom.: 29153 Cov.: 32 AF XY: 0.605 AC XY: 44915 AN XY: 74182

African (AFR) AF: 0.603 AC: 24984 AN: 41448

American (AMR) AF: 0.586 AC: 8928 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2213 AN: 3468

East Asian (EAS) AF: 0.244 AC: 1261 AN: 5170

South Asian (SAS) AF: 0.480 AC: 2317 AN: 4828

European-Finnish (FIN) AF: 0.574 AC: 6038 AN: 10514

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.666 AC: 45145 AN: 67830

Other (OTH) AF: 0.626 AC: 1315 AN: 2102

Alfa AF: 0.648 Hom.: 98501

Bravo AF: 0.616

Asia WGS AF: 0.409 AC: 1421 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.37
PhyloP100		-0.80

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: rs4532399;

hg19: chr5-40467272;