rs10866527

Variant names:

• chr5-1891686-C-T
• rs10866527
• ENST00000514569.1:n.108+3404C>T

Variant summary

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

The ENST00000514569.1(CTD-2194D22.4):​n.108+3404C>T variant causes a intron 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 ENST00000514569.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00
• Publications: 11 publications found

Genes affected

CTD-2194D22.4 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CTD-2194D22.4	NR_109912.1	n.109+3404C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CTD-2194D22.4	ENST00000514569.1	n.108+3404C>T		intron_variant	Intron 2 of 3	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

African (AFR) AF: 0.314 AC: 13040 AN: 41498

American (AMR) AF: 0.496 AC: 7585 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1611 AN: 3472

East Asian (EAS) AF: 0.353 AC: 1824 AN: 5162

South Asian (SAS) AF: 0.505 AC: 2434 AN: 4822

European-Finnish (FIN) AF: 0.521 AC: 5516 AN: 10592

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32181 AN: 67972

Other (OTH) AF: 0.446 AC: 942 AN: 2112

Alfa AF: 0.464 Hom.: 12640

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
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs10866527; hg19: chr5-1891800;