5-4725035-G-A

Position:

• chr5-4725035-G-A

Variant summary

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

The ENST00000507435.1(ENSG00000248973):​n.429+59836C>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 0.818 in 152,142 control chromosomes in the GnomAD database, including 51,167 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 0.82 (51167 hom., cov: 32)
• Consequence: ENST00000507435.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000507435.1	n.429+59836C>T		intron_variant, non_coding_transcript_variant		5
	ENST00000651524.1	n.212-17666C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.818 AC: 124388 AN: 152024 Hom.: 51133 Cov.: 32

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.929

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.917

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.841

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.818 AC: 124475 AN: 152142 Hom.: 51167 Cov.: 32 AF XY: 0.812 AC XY: 60350 AN XY: 74364

Gnomad4 AFR AF: 0.827

Gnomad4 AMR AF: 0.729

Gnomad4 ASJ AF: 0.917

Gnomad4 EAS AF: 0.651

Gnomad4 SAS AF: 0.842

Gnomad4 FIN AF: 0.792

Gnomad4 NFE AF: 0.841

Gnomad4 OTH AF: 0.839

Alfa AF: 0.796 Hom.: 4990

Bravo AF: 0.812

Asia WGS AF: 0.760 AC: 2645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.46
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1393122; hg19: chr5-4725148;