chr12-68100048-C-T

Variant names:

• chr12-68100048-C-T
• rs10492198
• ENST00000536914.1:n.336+73340C>T

Variant summary

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

The ENST00000536914.1(IFNG-AS1):​n.336+73340C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 151,732 control chromosomes in the GnomAD database, including 9,218 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 0.31 (9218 hom., cov: 31)
• Consequence: IFNG-AS1 ENST00000536914.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 3 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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFNG-AS1	ENST00000536914.1	n.336+73340C>T		intron_variant	Intron 5 of 5	5
ENSG00000301254	ENST00000777404.1	n.168-4077G>A		intron_variant	Intron 1 of 2
ENSG00000301254	ENST00000777405.1	n.188-4077G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47479 AN: 151614 Hom.: 9209 Cov.: 31

Gnomad AFR AF: 0.0838

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.313 AC: 47491 AN: 151732 Hom.: 9218 Cov.: 31 AF XY: 0.323 AC XY: 23929 AN XY: 74142

African (AFR) AF: 0.0836 AC: 3462 AN: 41394

American (AMR) AF: 0.476 AC: 7257 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1234 AN: 3468

East Asian (EAS) AF: 0.352 AC: 1810 AN: 5136

South Asian (SAS) AF: 0.538 AC: 2583 AN: 4802

European-Finnish (FIN) AF: 0.428 AC: 4489 AN: 10490

Middle Eastern (MID) AF: 0.329 AC: 96 AN: 292

European-Non Finnish (NFE) AF: 0.375 AC: 25469 AN: 67884

Other (OTH) AF: 0.334 AC: 705 AN: 2112

Alfa AF: 0.343 Hom.: 1279

Bravo AF: 0.306

Asia WGS AF: 0.442 AC: 1533 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.84
DANN	Benign	0.72
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10492198; hg19: chr12-68493828;