rs12778872

Variant names:

• chr10-87597176-C-A
• rs12778872
• ENST00000446794.1:n.32-5433G>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

Genes affected

ENSG00000223761 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105378412	XR_946171.2	n.86+642C>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000223761	ENST00000446794.1	n.32-5433G>T		intron_variant	Intron 1 of 1	3
ENSG00000225913	ENST00000804457.1	n.103-9125C>A		intron_variant	Intron 1 of 4
ENSG00000225913	ENST00000804458.1	n.113+642C>A		intron_variant	Intron 1 of 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

African (AFR) AF: 0.0698 AC: 2898 AN: 41504

American (AMR) AF: 0.132 AC: 2016 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 473 AN: 3468

East Asian (EAS) AF: 0.157 AC: 806 AN: 5138

South Asian (SAS) AF: 0.123 AC: 593 AN: 4814

European-Finnish (FIN) AF: 0.147 AC: 1559 AN: 10586

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10817 AN: 67986

Other (OTH) AF: 0.146 AC: 308 AN: 2114

Alfa AF: 0.150 Hom.: 7205

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
PhyloP100		0.079
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs12778872; hg19: chr10-89356933;