10-29131476-C-T

Variant names:

• chr10-29131476-C-T
• rs950000
• ENST00000766991.1:n.202-15659C>T

Variant summary

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

The ENST00000766991.1(ENSG00000299869):​n.202-15659C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 152,004 control chromosomes in the GnomAD database, including 15,479 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 0.45 (15479 hom., cov: 33)
• Consequence: ENSG00000299869 ENST00000766991.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.531
• Publications: 4 publications found

Genes affected

ENSG00000299869 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.549 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
ENSG00000299869	ENST00000766991.1	n.202-15659C>T		intron_variant	Intron 2 of 2
ENSG00000299869	ENST00000766992.1	n.239-2838C>T		intron_variant	Intron 2 of 3
ENSG00000299883	ENST00000767191.1	n.136-157C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68399 AN: 151886 Hom.: 15482 Cov.: 33

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.450 AC: 68396 AN: 152004 Hom.: 15479 Cov.: 33 AF XY: 0.454 AC XY: 33716 AN XY: 74296

African (AFR) AF: 0.439 AC: 18186 AN: 41450

American (AMR) AF: 0.493 AC: 7540 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1873 AN: 3468

East Asian (EAS) AF: 0.358 AC: 1843 AN: 5150

South Asian (SAS) AF: 0.567 AC: 2732 AN: 4822

European-Finnish (FIN) AF: 0.406 AC: 4291 AN: 10566

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.445 AC: 30230 AN: 67948

Other (OTH) AF: 0.507 AC: 1070 AN: 2112

Alfa AF: 0.454 Hom.: 11969

Bravo AF: 0.455

Asia WGS AF: 0.451 AC: 1570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.24
DANN	Benign	0.73
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs950000; hg19: chr10-29420405;