5-40429090-C-T

Variant names:

• chr5-40429090-C-T
• rs6880934
• ENST00000637776.2:n.360-842C>T

Variant summary

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

The ENST00000691408.1(ENSG00000283286):​n.187-842C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 151,926 control chromosomes in the GnomAD database, including 20,461 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 0.51 (20461 hom., cov: 32)
• Consequence: ENSG00000283286 ENST00000691408.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780
• Publications: 6 publications found

Genes affected

ENSG00000283286 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000691408.1. 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
	ENSG00000283286	ENST00000637776.2	TSL:5	n.360-842C>T		intron	N/A
	ENSG00000283286	ENST00000691408.1		n.187-842C>T		intron	N/A
	ENSG00000283286	ENST00000809813.1		n.460-842C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78022 AN: 151808 Hom.: 20435 Cov.: 32

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.554

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.514 AC: 78098 AN: 151926 Hom.: 20461 Cov.: 32 AF XY: 0.508 AC XY: 37752 AN XY: 74258

African (AFR) AF: 0.471 AC: 19485 AN: 41392

American (AMR) AF: 0.580 AC: 8854 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.633 AC: 2193 AN: 3466

East Asian (EAS) AF: 0.256 AC: 1321 AN: 5168

South Asian (SAS) AF: 0.510 AC: 2458 AN: 4824

European-Finnish (FIN) AF: 0.401 AC: 4224 AN: 10542

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.554 AC: 37623 AN: 67952

Other (OTH) AF: 0.557 AC: 1176 AN: 2112

Alfa AF: 0.551 Hom.: 72122

Bravo AF: 0.528

Asia WGS AF: 0.407 AC: 1416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.3
DANN	Benign	0.71
PhyloP100		0.078

Splicing

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

Other links and lift over

dbSNP: rs6880934; hg19: chr5-40429192;