16-10256280-A-G

Variant names:

• chr16-10256280-A-G
• rs4456502
• ENST00000649384.2:n.137+6732T>C

Variant summary

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

The ENST00000649384.2(ENSG00000285543):​n.137+6732T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,106 control chromosomes in the GnomAD database, including 8,158 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 0.32 (8158 hom., cov: 32)
• Consequence: ENSG00000285543 ENST00000649384.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15
• Publications: 2 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=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.353 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.137+6732T>C		intron_variant	Intron 1 of 4
ENSG00000285543	ENST00000784408.1	n.139+516T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49355 AN: 151986 Hom.: 8149 Cov.: 32

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.325 AC: 49397 AN: 152106 Hom.: 8158 Cov.: 32 AF XY: 0.324 AC XY: 24121 AN XY: 74368

African (AFR) AF: 0.281 AC: 11660 AN: 41502

American (AMR) AF: 0.290 AC: 4425 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1353 AN: 3466

East Asian (EAS) AF: 0.220 AC: 1139 AN: 5178

South Asian (SAS) AF: 0.302 AC: 1453 AN: 4816

European-Finnish (FIN) AF: 0.378 AC: 4000 AN: 10580

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24280 AN: 67980

Other (OTH) AF: 0.357 AC: 754 AN: 2112

Alfa AF: 0.344 Hom.: 8513

Bravo AF: 0.319

Asia WGS AF: 0.282 AC: 983 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0080
DANN	Benign	0.40
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs4456502; hg19: chr16-10350137;