rs10514821

Positions:

• chr9-12984757-A-G

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, non coding transcript 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: ENST00000649120.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000649120.1	n.885+18678T>C		intron_variant, non_coding_transcript_variant

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;