4-132206497-T-C

Variant names:

• chr4-132206497-T-C
• rs348085
• ENST00000652009.1:n.177+129224A>G

Variant summary

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

The ENST00000652009.1(ENSG00000251598):​n.177+129224A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 151,530 control chromosomes in the GnomAD database, including 10,139 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 0.36 (10139 hom., cov: 31)
• Consequence: ENSG00000251598 ENST00000652009.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.39

Genes affected

ENSG00000251598 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000251598	ENST00000652009.1	n.177+129224A>G		intron_variant	Intron 2 of 8

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55156 AN: 151412 Hom.: 10126 Cov.: 31

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.400

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.364 AC: 55210 AN: 151530 Hom.: 10139 Cov.: 31 AF XY: 0.360 AC XY: 26634 AN XY: 74060

Gnomad4 AFR AF: 0.390

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.515

Gnomad4 EAS AF: 0.213

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.373

Gnomad4 OTH AF: 0.359

Alfa AF: 0.363 Hom.: 1248

Bravo AF: 0.371

Asia WGS AF: 0.259 AC: 890 AN: 3440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.0
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs348085; hg19: chr4-133127652;