rs10514542

Variant names:

• chr16-82524079-G-C
• rs10514542
• ENST00000650164.1:n.585-13535C>G

Your query was ambiguous. Multiple possible variants found:

• chr16-82524079-G-C
• chr16-82524079-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000650164.1(ENSG00000261285):​n.585-13535C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,036 control chromosomes in the GnomAD database, including 4,906 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 0.25 (4906 hom., cov: 33)
• Consequence: ENSG00000261285 ENST00000650164.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730

Genes affected

ENSG00000261285 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.272 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
ENSG00000261285	ENST00000650164.1	n.585-13535C>G		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37233 AN: 151918 Hom.: 4900 Cov.: 33

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.00676

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.245 AC: 37251 AN: 152036 Hom.: 4906 Cov.: 33 AF XY: 0.240 AC XY: 17836 AN XY: 74292

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.00678

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.234

Alfa AF: 0.145 Hom.: 282

Bravo AF: 0.241

Asia WGS AF: 0.116 AC: 402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.2
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10514542; hg19: chr16-82557684;