rs10866527

Positions:

• chr5-1891686-C-T

Variant summary

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

The NR_109912.1(CTD-2194D22.4):​n.109+3404C>T 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 0.431 in 152,118 control chromosomes in the GnomAD database, including 14,710 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 0.43 (14710 hom., cov: 33)
• Consequence: CTD-2194D22.4 NR_109912.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00

Genes affected

CTD-2194D22.4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CTD-2194D22.4	NR_109912.1	n.109+3404C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CTD-2194D22.4	ENST00000514569.1	n.108+3404C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65586 AN: 152000 Hom.: 14698 Cov.: 33

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.431 AC: 65636 AN: 152118 Hom.: 14710 Cov.: 33 AF XY: 0.439 AC XY: 32609 AN XY: 74350

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.496

Gnomad4 ASJ AF: 0.464

Gnomad4 EAS AF: 0.353

Gnomad4 SAS AF: 0.505

Gnomad4 FIN AF: 0.521

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.446

Alfa AF: 0.464 Hom.: 8151

Bravo AF: 0.422

Asia WGS AF: 0.450 AC: 1564 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.5
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10866527; hg19: chr5-1891800;