rs10514821

Variant names:

• chr9-12984757-A-G
• rs10514821
• ENST00000649120.1:n.885+18678T>C

Variant summary

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

The ENST00000649120.1(ENSG00000285637):​n.885+18678T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0752 in 152,146 control chromosomes in the GnomAD database, including 1,178 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 0.075 (1178 hom., cov: 32)
• Consequence: ENSG00000285637 ENST00000649120.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

Genes affected

ENSG00000285637 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.225 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
ENSG00000285637	ENST00000649120.1	n.885+18678T>C		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.0751 AC: 11411 AN: 152028 Hom.: 1177 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0687

Gnomad ASJ AF: 0.0363

Gnomad EAS AF: 0.0137

Gnomad SAS AF: 0.0192

Gnomad FIN AF: 0.00631

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00619

Gnomad OTH AF: 0.0550

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

GnomAD4 genome AF: 0.0752 AC: 11435 AN: 152146 Hom.: 1178 Cov.: 32 AF XY: 0.0738 AC XY: 5491 AN XY: 74388

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.0685

Gnomad4 ASJ AF: 0.0363

Gnomad4 EAS AF: 0.0137

Gnomad4 SAS AF: 0.0193

Gnomad4 FIN AF: 0.00631

Gnomad4 NFE AF: 0.00619

Gnomad4 OTH AF: 0.0544

Alfa AF: 0.0415 Hom.: 189

Bravo AF: 0.0871

Asia WGS AF: 0.0340 AC: 119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.8
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10514821; hg19: chr9-12984756;