rs12778872

Positions:

• chr10-87597176-C-A
• chr10-87597176-C-T

Variant summary

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

The ENST00000446794.1(ENSG00000223761):​n.32-5433G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,100 control chromosomes in the GnomAD database, including 1,403 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 0.13 (1403 hom., cov: 32)
• Consequence: ENSG00000223761 ENST00000446794.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790

Genes affected

ENSG00000223761 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378412	XR_946171.2	n.86+642C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000223761	ENST00000446794.1	n.32-5433G>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19676 AN: 151982 Hom.: 1402 Cov.: 32

Gnomad AFR AF: 0.0700

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.129 AC: 19685 AN: 152100 Hom.: 1403 Cov.: 32 AF XY: 0.131 AC XY: 9711 AN XY: 74358

Gnomad4 AFR AF: 0.0698

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.157

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.146

Alfa AF: 0.153 Hom.: 3475

Bravo AF: 0.126

Asia WGS AF: 0.167 AC: 578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.0
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12778872; hg19: chr10-89356933;