ENST00000512546.1:n.53+4378A>G

Variant names:

• chr4-59157264-A-G
• rs371989
• ENST00000512546.1:n.53+4378A>G

Variant summary

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

The ENST00000512546.1(ENSG00000249111):​n.53+4378A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 151,332 control chromosomes in the GnomAD database, including 6,567 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 0.28 (6567 hom., cov: 31)
• Consequence: ENSG00000249111 ENST00000512546.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.48

Genes affected

ENSG00000249111 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.374 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
ENSG00000249111	ENST00000512546.1	n.53+4378A>G		intron_variant	Intron 1 of 1	3
ENSG00000286097	ENST00000651732.1	n.241-4684T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42512 AN: 151218 Hom.: 6563 Cov.: 31

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.191

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.281 AC: 42520 AN: 151332 Hom.: 6567 Cov.: 31 AF XY: 0.281 AC XY: 20785 AN XY: 73906

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.388

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.304

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.288

Alfa AF: 0.176 Hom.: 381

Bravo AF: 0.285

Asia WGS AF: 0.273 AC: 942 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.3
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs371989; hg19: chr4-60022982;