chr5-2077466-C-T

Variant names:

• chr5-2077466-C-T
• rs10866530
• ENST00000653000.1:n.666-19773C>T

Variant summary

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

The ENST00000653000.1(ENSG00000248994):​n.666-19773C>T variant causes a intron 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: ENSG00000248994 ENST00000653000.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.694
• Publications: 2 publications found

Genes affected

ENSG00000248994 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105374618	NR_171679.1	n.1692+5814C>T		intron_variant	Intron 7 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248994	ENST00000653000.1	n.666-19773C>T		intron_variant	Intron 2 of 8
ENSG00000248994	ENST00000657760.1	n.3091+5814C>T		intron_variant	Intron 4 of 7
ENSG00000248994	ENST00000660496.1	n.276+5814C>T		intron_variant	Intron 1 of 6
ENSG00000248994	ENST00000752785.1	n.455+5814C>T		intron_variant	Intron 3 of 3

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

African (AFR) AF: 0.274 AC: 11343 AN: 41408

American (AMR) AF: 0.320 AC: 4886 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1687 AN: 3466

East Asian (EAS) AF: 0.607 AC: 3142 AN: 5176

South Asian (SAS) AF: 0.471 AC: 2261 AN: 4802

European-Finnish (FIN) AF: 0.425 AC: 4473 AN: 10518

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.389 AC: 26403 AN: 67912

Other (OTH) AF: 0.382 AC: 803 AN: 2104

Alfa AF: 0.390 Hom.: 9684

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
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs10866530; hg19: chr5-2077580;