rs1992489

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr4-77452729-T-C
• chr4-77452729-T-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

ENSG00000249036 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.534 AC: 22118 AN: 41396

American (AMR) AF: 0.817 AC: 12467 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.780 AC: 2705 AN: 3470

East Asian (EAS) AF: 0.844 AC: 4345 AN: 5146

South Asian (SAS) AF: 0.828 AC: 3982 AN: 4812

European-Finnish (FIN) AF: 0.839 AC: 8872 AN: 10580

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.832 AC: 56554 AN: 67992

Other (OTH) AF: 0.782 AC: 1651 AN: 2110

Alfa AF: 0.808 Hom.: 36492

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
PhyloP100		-0.013

Splicing

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

Other links and lift over

dbSNP: rs1992489; hg19: chr4-78373883;