5-143561127-T-G

Position:

• chr5-143561127-T-G

Variant summary

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

The variant allele was found at a frequency of 0.0393 in 152,262 control chromosomes in the GnomAD database, including 155 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 0.039 (155 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.143561127T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000251205	ENST00000514942.2	n.219-179T>G		intron_variant		5
ENSG00000251205	ENST00000661617.1	n.242-179T>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0394 AC: 5988 AN: 152144 Hom.: 156 Cov.: 32

Gnomad AFR AF: 0.0609

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.0311

Gnomad ASJ AF: 0.0130

Gnomad EAS AF: 0.00865

Gnomad SAS AF: 0.0244

Gnomad FIN AF: 0.0139

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0360

Gnomad OTH AF: 0.0368

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

GnomAD4 genome AF: 0.0393 AC: 5987 AN: 152262 Hom.: 155 Cov.: 32 AF XY: 0.0373 AC XY: 2775 AN XY: 74456

Gnomad4 AFR AF: 0.0607

Gnomad4 AMR AF: 0.0310

Gnomad4 ASJ AF: 0.0130

Gnomad4 EAS AF: 0.00886

Gnomad4 SAS AF: 0.0244

Gnomad4 FIN AF: 0.0139

Gnomad4 NFE AF: 0.0360

Gnomad4 OTH AF: 0.0369

Alfa AF: 0.00614 Hom.: 69

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	2.2
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11955681; hg19: chr5-142940692;