4-132843587-C-T

Position:

• chr4-132843587-C-T

Variant summary

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

The ENST00000509628.1(ENSG00000251488):​n.165-6393G>A 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 0.217 in 151,994 control chromosomes in the GnomAD database, including 4,388 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 0.22 (4388 hom., cov: 33)
• Consequence: ENST00000509628.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.582 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
	ENST00000509628.1	n.165-6393G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32961 AN: 151876 Hom.: 4366 Cov.: 33

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.179

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.217 AC: 33036 AN: 151994 Hom.: 4388 Cov.: 33 AF XY: 0.223 AC XY: 16545 AN XY: 74292

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.600

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.215

Alfa AF: 0.157 Hom.: 4106

Bravo AF: 0.224

Asia WGS AF: 0.417 AC: 1449 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10518621; hg19: chr4-133764742;