rs10492201

Positions:

• chr12-67992086-G-A
• chr12-67992086-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_104124.1(IFNG-AS1):​n.135+2507G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,076 control chromosomes in the GnomAD database, including 1,158 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 0.11 (1158 hom., cov: 32)
• Consequence: IFNG-AS1 NR_104124.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IFNG-AS1	NR_104124.1	n.135+2507G>A		intron_variant, non_coding_transcript_variant
IFNG-AS1	NR_104125.1	n.135+2507G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IFNG-AS1	ENST00000536914.1	n.51+2507G>A		intron_variant, non_coding_transcript_variant		5
IFNG-AS1	ENST00000538665.5	n.135+2507G>A		intron_variant, non_coding_transcript_variant		2
IFNG-AS1	ENST00000541715.5	n.124+2507G>A		intron_variant, non_coding_transcript_variant		3
IFNG-AS1	ENST00000674322.1	n.127+2038G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16469 AN: 151958 Hom.: 1156 Cov.: 32

Gnomad AFR AF: 0.0350

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.0825

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.0900

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

GnomAD4 genome AF: 0.108 AC: 16464 AN: 152076 Hom.: 1158 Cov.: 32 AF XY: 0.108 AC XY: 8011 AN XY: 74334

Gnomad4 AFR AF: 0.0349

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.0825

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.0890

Alfa AF: 0.127 Hom.: 707

Bravo AF: 0.110

Asia WGS AF: 0.140 AC: 484 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10492201; hg19: chr12-68385866;