ENST00000649384.2:n.529+1108G>A

Variant names:

• chr16-10224674-C-T
• rs4780896
• ENST00000649384.2:n.529+1108G>A

Variant summary

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

The ENST00000649384.2(ENSG00000285543):​n.529+1108G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 151,870 control chromosomes in the GnomAD database, including 13,654 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 0.41 (13654 hom., cov: 32)
• Consequence: ENSG00000285543 ENST00000649384.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.268
• Publications: 1 publications found

Genes affected

ENSG00000285543 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.495 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
ENSG00000285543	ENST00000649384.2	n.529+1108G>A		intron_variant	Intron 3 of 4
ENSG00000285543	ENST00000784407.1	n.459+2735G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62118 AN: 151752 Hom.: 13651 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.0607

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.409 AC: 62140 AN: 151870 Hom.: 13654 Cov.: 32 AF XY: 0.406 AC XY: 30108 AN XY: 74216

African (AFR) AF: 0.302 AC: 12512 AN: 41382

American (AMR) AF: 0.332 AC: 5075 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.624 AC: 2161 AN: 3464

East Asian (EAS) AF: 0.0614 AC: 318 AN: 5176

South Asian (SAS) AF: 0.394 AC: 1897 AN: 4812

European-Finnish (FIN) AF: 0.467 AC: 4912 AN: 10514

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 33965 AN: 67944

Other (OTH) AF: 0.417 AC: 877 AN: 2102

Alfa AF: 0.477 Hom.: 29830

Bravo AF: 0.393

Asia WGS AF: 0.255 AC: 885 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.67
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs4780896; hg19: chr16-10318531;