rs1992489

chr4-77452729-T-Cchr4-77452729-T-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, non coding transcript 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: ENST00000513871.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000513871.1	n.122+41436A>G		intron_variant, non_coding_transcript_variant		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;