ENST00000635992.1:n.*116-16221A>C

Variant names:

• chr3-28560052-A-C
• rs4680758
• ENST00000635992.1:n.*116-16221A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000635992.1(ENSG00000283563):​n.*116-16221A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.758 in 149,422 control chromosomes in the GnomAD database, including 42,971 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 0.76 (42971 hom., cov: 28)
• Consequence: ENSG00000283563 ENST00000635992.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.433
• Publications: 2 publications found

Genes affected

ENSG00000283563 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.837 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986012	XM_047449399.1	c.*438-2314T>G		intron_variant	Intron 2 of 2		XP_047305355.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283563	ENST00000635992.1	n.*116-16221A>C		intron_variant	Intron 5 of 13	5		ENSP00000489994.1
ENSG00000309494	ENST00000841502.1	n.421-2314T>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.758 AC: 113174 AN: 149354 Hom.: 42951 Cov.: 28

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.801

Gnomad AMR AF: 0.755

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.859

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.724

Gnomad NFE AF: 0.733

Gnomad OTH AF: 0.751

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

GnomAD4 genome AF: 0.758 AC: 113218 AN: 149422 Hom.: 42971 Cov.: 28 AF XY: 0.761 AC XY: 55377 AN XY: 72790

African (AFR) AF: 0.789 AC: 32119 AN: 40728

American (AMR) AF: 0.755 AC: 11342 AN: 15030

Ashkenazi Jewish (ASJ) AF: 0.723 AC: 2507 AN: 3466

East Asian (EAS) AF: 0.802 AC: 4104 AN: 5116

South Asian (SAS) AF: 0.859 AC: 4077 AN: 4746

European-Finnish (FIN) AF: 0.745 AC: 7183 AN: 9642

Middle Eastern (MID) AF: 0.701 AC: 202 AN: 288

European-Non Finnish (NFE) AF: 0.733 AC: 49402 AN: 67424

Other (OTH) AF: 0.750 AC: 1555 AN: 2074

Alfa AF: 0.756 Hom.: 56032

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.38
DANN	Benign	0.40
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs4680758; hg19: chr3-28601543;