rs10777556

Variant names:

• chr12-93918315-C-T
• rs10777556
• ENST00000550687.1:n.60-9310G>A

Variant summary

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

The ENST00000550687.1(ENSG00000257283):​n.60-9310G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0726 in 152,020 control chromosomes in the GnomAD database, including 532 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 0.073 (532 hom., cov: 32)
• Consequence: ENSG00000257283 ENST00000550687.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 2 publications found

Genes affected

ENSG00000257283 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369911	NR_135017.1	n.63-9310G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257283	ENST00000550687.1	n.60-9310G>A		intron_variant	Intron 1 of 2	4
ENSG00000257283	ENST00000786429.1	n.197-9310G>A		intron_variant	Intron 2 of 3
ENSG00000257283	ENST00000786431.1	n.84+4247G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0725 AC: 11006 AN: 151902 Hom.: 530 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.0518

Gnomad ASJ AF: 0.0588

Gnomad EAS AF: 0.0187

Gnomad SAS AF: 0.0711

Gnomad FIN AF: 0.0653

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0499

Gnomad OTH AF: 0.0513

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

GnomAD4 genome AF: 0.0726 AC: 11036 AN: 152020 Hom.: 532 Cov.: 32 AF XY: 0.0732 AC XY: 5437 AN XY: 74316

African (AFR) AF: 0.129 AC: 5352 AN: 41448

American (AMR) AF: 0.0517 AC: 789 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0588 AC: 204 AN: 3472

East Asian (EAS) AF: 0.0181 AC: 94 AN: 5182

South Asian (SAS) AF: 0.0713 AC: 342 AN: 4794

European-Finnish (FIN) AF: 0.0653 AC: 690 AN: 10568

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0498 AC: 3389 AN: 67988

Other (OTH) AF: 0.0508 AC: 107 AN: 2106

Alfa AF: 0.0550 Hom.: 1050

Bravo AF: 0.0712

Asia WGS AF: 0.0490 AC: 170 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.18
DANN	Benign	0.45
PhyloP100		-1.0
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: rs10777556; hg19: chr12-94312091;