ENST00000513871.1:n.122+41436A>G

Variant names:

• chr4-77452729-T-C
• rs1992489
• ENST00000513871.1:n.122+41436A>G

Variant summary

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

The ENST00000513871.1(ENSG00000249036):​n.122+41436A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.748 in 151,980 control chromosomes in the GnomAD database, including 43,889 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 0.75 (43889 hom., cov: 30)
• Consequence: ENSG00000249036 ENST00000513871.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130

Genes affected

ENSG00000249036 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.826 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
ENSG00000249036	ENST00000513871.1	n.122+41436A>G		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.748 AC: 113653 AN: 151862 Hom.: 43864 Cov.: 30

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.817

Gnomad ASJ AF: 0.780

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.832

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.748 AC: 113728 AN: 151980 Hom.: 43889 Cov.: 30 AF XY: 0.751 AC XY: 55825 AN XY: 74314

Gnomad4 AFR AF: 0.534

Gnomad4 AMR AF: 0.817

Gnomad4 ASJ AF: 0.780

Gnomad4 EAS AF: 0.844

Gnomad4 SAS AF: 0.828

Gnomad4 FIN AF: 0.839

Gnomad4 NFE AF: 0.832

Gnomad4 OTH AF: 0.782

Alfa AF: 0.813 Hom.: 26965

Bravo AF: 0.738

Asia WGS AF: 0.831 AC: 2888 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.0
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1992489; hg19: chr4-78373883;