rs12515335

Variant names:

• chr5-8556975-T-C
• rs12515335
• ENST00000654467.2:n.488-3102T>C

Variant summary

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

The ENST00000654467.2(ENSG00000249782):​n.488-3102T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,058 control chromosomes in the GnomAD database, including 3,063 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 0.19 (3063 hom., cov: 32)
• Consequence: ENSG00000249782 ENST00000654467.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.443
• Publications: 0 publications found

Genes affected

ENSG00000249782 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654467.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105374647	NR_188263.1		n.604-3102T>C		intron	N/A
	LOC105374647	NR_188264.1		n.638-3102T>C		intron	N/A
	LOC105374647	NR_188265.1		n.436-3102T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000249782	ENST00000654467.2		n.488-3102T>C		intron	N/A
	ENSG00000249782	ENST00000657075.1		n.689-3102T>C		intron	N/A
	ENSG00000249782	ENST00000659580.1		n.651-3102T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28456 AN: 151940 Hom.: 3062 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.0137

Gnomad SAS AF: 0.0966

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.187 AC: 28479 AN: 152058 Hom.: 3063 Cov.: 32 AF XY: 0.184 AC XY: 13645 AN XY: 74332

African (AFR) AF: 0.116 AC: 4806 AN: 41522

American (AMR) AF: 0.170 AC: 2593 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 803 AN: 3468

East Asian (EAS) AF: 0.0137 AC: 71 AN: 5188

South Asian (SAS) AF: 0.0971 AC: 469 AN: 4828

European-Finnish (FIN) AF: 0.224 AC: 2356 AN: 10522

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.246 AC: 16701 AN: 67936

Other (OTH) AF: 0.218 AC: 460 AN: 2112

Alfa AF: 0.220 Hom.: 3304

Bravo AF: 0.181

Asia WGS AF: 0.0680 AC: 236 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.74
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs12515335; hg19: chr5-8557087;