12-68188392-C-T

Variant names:

• chr12-68188392-C-T
• rs4913277
• ENST00000536914.1:n.337-46137C>T

Variant summary

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

The XR_001749193.2(LOC105369818):​n.3040+2448C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.609 in 151,414 control chromosomes in the GnomAD database, including 29,133 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 0.61 (29133 hom., cov: 28)
• Consequence: LOC105369818 XR_001749193.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213
• Publications: 6 publications found

Genes affected

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

LOC105369818 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000536914.1. 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.337-46137C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.609 AC: 92149 AN: 151296 Hom.: 29083 Cov.: 28

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.609 AC: 92255 AN: 151414 Hom.: 29133 Cov.: 28 AF XY: 0.599 AC XY: 44298 AN XY: 73944

African (AFR) AF: 0.732 AC: 30151 AN: 41216

American (AMR) AF: 0.478 AC: 7268 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.637 AC: 2207 AN: 3466

East Asian (EAS) AF: 0.233 AC: 1194 AN: 5118

South Asian (SAS) AF: 0.595 AC: 2843 AN: 4780

European-Finnish (FIN) AF: 0.453 AC: 4725 AN: 10432

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.615 AC: 41775 AN: 67884

Other (OTH) AF: 0.617 AC: 1294 AN: 2096

Alfa AF: 0.614 Hom.: 124228

Bravo AF: 0.612

Asia WGS AF: 0.501 AC: 1742 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.2
DANN	Benign	0.68
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs4913277; hg19: chr12-68582172;