5-40429090-C-T

Position:

• chr5-40429090-C-T

Variant summary

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

The ENST00000691408.1(ENSG00000283286):​n.187-842C>T variant causes a intron, non coding transcript 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: ENST00000691408.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000691408.1	n.187-842C>T		intron_variant, non_coding_transcript_variant
	ENST00000637776.1	n.63-842C>T		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.471

Gnomad4 AMR AF: 0.580

Gnomad4 ASJ AF: 0.633

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.510

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.554

Gnomad4 OTH AF: 0.557

Alfa AF: 0.555 Hom.: 47429

Bravo AF: 0.528

Asia WGS AF: 0.407 AC: 1416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6880934; hg19: chr5-40429192;