rs12327115

Variant names:

• chr18-66225371-G-A
• rs12327115
• ENST00000748761.1:n.294-4962C>T

Variant summary

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

The ENST00000748761.1(ENSG00000297542):​n.294-4962C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 151,878 control chromosomes in the GnomAD database, including 5,320 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 0.26 (5320 hom., cov: 32)
• Consequence: ENSG00000297542 ENST00000748761.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.97
• Publications: 0 publications found

Genes affected

ENSG00000297542 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000748761.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297542	ENST00000748761.1		n.294-4962C>T		intron	N/A
	ENSG00000297542	ENST00000748762.1		n.412-4962C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39766 AN: 151760 Hom.: 5320 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.262 AC: 39781 AN: 151878 Hom.: 5320 Cov.: 32 AF XY: 0.259 AC XY: 19240 AN XY: 74240

African (AFR) AF: 0.262 AC: 10826 AN: 41362

American (AMR) AF: 0.274 AC: 4172 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 872 AN: 3468

East Asian (EAS) AF: 0.105 AC: 544 AN: 5174

South Asian (SAS) AF: 0.377 AC: 1814 AN: 4810

European-Finnish (FIN) AF: 0.192 AC: 2031 AN: 10552

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18554 AN: 67948

Other (OTH) AF: 0.277 AC: 583 AN: 2108

Alfa AF: 0.259 Hom.: 678

Bravo AF: 0.266

Asia WGS AF: 0.270 AC: 940 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.0
DANN	Benign	0.60
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs12327115; hg19: chr18-63892608;