rs10777477

Variant names:

• chr12-93187914-C-A
• rs10777477
• ENST00000547432.1:n.316+2353G>T

Variant summary

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

The ENST00000547432.1(ENSG00000257252):​n.316+2353G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,012 control chromosomes in the GnomAD database, including 3,407 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 0.20 (3407 hom., cov: 32)
• Consequence: ENSG00000257252 ENST00000547432.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.474
• Publications: 3 publications found

Genes affected

ENSG00000257252 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000547432.1. 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
	LOC643339	NR_040096.1		n.427+27668G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000257252	ENST00000547432.1	TSL:3	n.316+2353G>T		intron	N/A
	ENSG00000257252	ENST00000549930.1	TSL:5	n.98+27668G>T		intron	N/A
	ENSG00000257252	ENST00000652973.2		n.291+2353G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30118 AN: 151892 Hom.: 3396 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.0769

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.198 AC: 30163 AN: 152012 Hom.: 3407 Cov.: 32 AF XY: 0.199 AC XY: 14752 AN XY: 74298

African (AFR) AF: 0.304 AC: 12585 AN: 41428

American (AMR) AF: 0.142 AC: 2169 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 489 AN: 3468

East Asian (EAS) AF: 0.109 AC: 563 AN: 5180

South Asian (SAS) AF: 0.188 AC: 907 AN: 4818

European-Finnish (FIN) AF: 0.155 AC: 1639 AN: 10560

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11255 AN: 67968

Other (OTH) AF: 0.193 AC: 409 AN: 2114

Alfa AF: 0.173 Hom.: 2829

Bravo AF: 0.201

Asia WGS AF: 0.140 AC: 487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.39
DANN	Benign	0.76
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs10777477; hg19: chr12-93581690;