rs827401

Variant names:

• chr10-8656867-G-A
• rs827401
• ENST00000750865.1:n.104+2248C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-8656867-G-A
• chr10-8656867-G-C
• chr10-8656867-G-T

Variant summary

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

The ENST00000750865.1(ENSG00000297769):​n.104+2248C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 151,786 control chromosomes in the GnomAD database, including 7,193 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 0.30 (7192 hom., cov: 31)
  • Exomes 𝑓: 0.60 (1 hom.)
• Consequence: ENSG00000297769 ENST00000750865.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.831
• Publications: 8 publications found

Genes affected

ENSG00000297769 (HGNC:):

RNA5SP299 (HGNC:43199): (RNA, 5S ribosomal pseudogene 299)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.44 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
ENSG00000297769	ENST00000750865.1	n.104+2248C>T		intron_variant	Intron 1 of 3
ENSG00000297769	ENST00000750866.1	n.102+2248C>T		intron_variant	Intron 1 of 2
RNA5SP299	ENST00000391203.1	n.-36C>T		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46191 AN: 151658 Hom.: 7168 Cov.: 31

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.316

GnomAD4 exome AF: 0.600 AC: 6 AN: 10 Hom.: 1 Cov.: 0 AF XY: 0.667 AC XY: 4 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 3 AN: 6

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.750 AC: 3 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.305 AC: 46246 AN: 151776 Hom.: 7192 Cov.: 31 AF XY: 0.305 AC XY: 22589 AN XY: 74108

African (AFR) AF: 0.252 AC: 10433 AN: 41404

American (AMR) AF: 0.341 AC: 5188 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1051 AN: 3468

East Asian (EAS) AF: 0.456 AC: 2347 AN: 5150

South Asian (SAS) AF: 0.301 AC: 1442 AN: 4794

European-Finnish (FIN) AF: 0.282 AC: 2957 AN: 10494

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21743 AN: 67928

Other (OTH) AF: 0.321 AC: 675 AN: 2106

Alfa AF: 0.311 Hom.: 3601

Bravo AF: 0.305

Asia WGS AF: 0.380 AC: 1321 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.2
DANN	Benign	0.58
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs827401; hg19: chr10-8698830;