rs10866530

Positions:

• chr5-2077466-C-T

Variant summary

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

The NR_171679.1(LOC105374618):​n.1692+5814C>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 0.365 in 151,878 control chromosomes in the GnomAD database, including 10,568 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 0.37 (10568 hom., cov: 33)
• Consequence: LOC105374618 NR_171679.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.694

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374618	NR_171679.1	n.1692+5814C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000653000.1	n.666-19773C>T		intron_variant, non_coding_transcript_variant
	ENST00000657760.1	n.3091+5814C>T		intron_variant, non_coding_transcript_variant
	ENST00000660496.1	n.276+5814C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55446 AN: 151756 Hom.: 10570 Cov.: 33

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.365 AC: 55468 AN: 151878 Hom.: 10568 Cov.: 33 AF XY: 0.369 AC XY: 27368 AN XY: 74236

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.607

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.425

Gnomad4 NFE AF: 0.389

Gnomad4 OTH AF: 0.382

Alfa AF: 0.389 Hom.: 6823

Bravo AF: 0.353

Asia WGS AF: 0.523 AC: 1811 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10866530; hg19: chr5-2077580;