10-90947429-G-T

Variant names:

• chr10-90947429-G-T
• rs12776792
• ENST00000846221.1:n.83+12368G>T

Variant summary

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

The NR_131214.1(XLOC_008559):​n.109+21G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 152,050 control chromosomes in the GnomAD database, including 10,955 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 (10955 hom., cov: 32)
• Consequence: XLOC_008559 NR_131214.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254
• Publications: 1 publications found

Genes affected

ENSG00000225519 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_131214.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	XLOC_008559	NR_131214.1		n.109+21G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000225519	ENST00000846221.1		n.83+12368G>T		intron	N/A
	ENSG00000225519	ENST00000846283.1		n.201-503G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56379 AN: 151932 Hom.: 10939 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.371 AC: 56419 AN: 152050 Hom.: 10955 Cov.: 32 AF XY: 0.383 AC XY: 28439 AN XY: 74322

African (AFR) AF: 0.371 AC: 15394 AN: 41454

American (AMR) AF: 0.390 AC: 5962 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1240 AN: 3468

East Asian (EAS) AF: 0.756 AC: 3919 AN: 5182

South Asian (SAS) AF: 0.510 AC: 2450 AN: 4808

European-Finnish (FIN) AF: 0.394 AC: 4162 AN: 10564

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.327 AC: 22196 AN: 67978

Other (OTH) AF: 0.351 AC: 741 AN: 2112

Alfa AF: 0.344 Hom.: 1378

Bravo AF: 0.364

Asia WGS AF: 0.614 AC: 2133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.29
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs12776792; hg19: chr10-92707186;