5-143625823-C-T

Position:

• chr5-143625823-C-T

Variant summary

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

The ENST00000503323.1(ENSG00000249881):​n.104+20092C>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 0.106 in 152,178 control chromosomes in the GnomAD database, including 1,073 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 0.11 (1073 hom., cov: 32)
• Consequence: ENST00000503323.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.192 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
	ENST00000503323.1	n.104+20092C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16190 AN: 152060 Hom.: 1072 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0778

Gnomad ASJ AF: 0.0936

Gnomad EAS AF: 0.0302

Gnomad SAS AF: 0.0957

Gnomad FIN AF: 0.0454

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0765

Gnomad OTH AF: 0.0980

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

GnomAD4 genome AF: 0.106 AC: 16202 AN: 152178 Hom.: 1073 Cov.: 32 AF XY: 0.104 AC XY: 7717 AN XY: 74406

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.0777

Gnomad4 ASJ AF: 0.0936

Gnomad4 EAS AF: 0.0303

Gnomad4 SAS AF: 0.0954

Gnomad4 FIN AF: 0.0454

Gnomad4 NFE AF: 0.0765

Gnomad4 OTH AF: 0.0979

Alfa AF: 0.0411 Hom.: 39

Bravo AF: 0.113

Asia WGS AF: 0.0790 AC: 273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.24
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17100506; hg19: chr5-143005388;