rs12815372

Variant names:

• chr12-68085433-G-A
• rs12815372
• ENST00000536914.1:n.336+58725G>A

Variant summary

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

The ENST00000777404.1(ENSG00000301254):​n.263+10443C>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 152,042 control chromosomes in the GnomAD database, including 6,333 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 (6333 hom., cov: 31)
• Consequence: ENSG00000301254 ENST00000777404.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310
• Publications: 9 publications found

Genes affected

IFNG-AS1 (HGNC:43910): (IFNG antisense RNA 1)

ENSG00000301254 (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 = 0.373 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000777404.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFNG-AS1	ENST00000536914.1	TSL:5	n.336+58725G>A		intron	N/A
	ENSG00000301254	ENST00000777404.1		n.263+10443C>T		intron	N/A
	ENSG00000301254	ENST00000777405.1		n.283+10443C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39881 AN: 151924 Hom.: 6331 Cov.: 31

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.262 AC: 39893 AN: 152042 Hom.: 6333 Cov.: 31 AF XY: 0.255 AC XY: 18944 AN XY: 74308

African (AFR) AF: 0.123 AC: 5101 AN: 41502

American (AMR) AF: 0.209 AC: 3192 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1029 AN: 3468

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5176

South Asian (SAS) AF: 0.123 AC: 592 AN: 4820

European-Finnish (FIN) AF: 0.326 AC: 3442 AN: 10552

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.377 AC: 25639 AN: 67944

Other (OTH) AF: 0.265 AC: 560 AN: 2114

Alfa AF: 0.313 Hom.: 1937

Bravo AF: 0.247

Asia WGS AF: 0.0560 AC: 195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.61
PhyloP100		0.031

Splicing

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

Other links and lift over

dbSNP: rs12815372; hg19: chr12-68479213;