rs971545

Variant names:

• chr12-68197905-A-G
• rs971545
• XR_001749193.2:n.4855A>G

Variant summary

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

The XR_001749193.2(LOC105369818):​n.4855A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 152,030 control chromosomes in the GnomAD database, including 11,477 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 0.37 (11477 hom., cov: 31)
• Consequence: LOC105369818 XR_001749193.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 8 publications found

Genes affected

LOC105369818 (HGNC:):

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369818	XR_001749193.2	n.4855A>G		non_coding_transcript_exon_variant	Exon 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFNG-AS1	ENST00000536914.1	n.337-36624A>G		intron_variant	Intron 5 of 5	5

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56251 AN: 151912 Hom.: 11468 Cov.: 31

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.370 AC: 56264 AN: 152030 Hom.: 11477 Cov.: 31 AF XY: 0.362 AC XY: 26874 AN XY: 74300

African (AFR) AF: 0.222 AC: 9194 AN: 41480

American (AMR) AF: 0.354 AC: 5406 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1580 AN: 3466

East Asian (EAS) AF: 0.146 AC: 752 AN: 5160

South Asian (SAS) AF: 0.349 AC: 1679 AN: 4812

European-Finnish (FIN) AF: 0.352 AC: 3719 AN: 10562

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.478 AC: 32460 AN: 67956

Other (OTH) AF: 0.410 AC: 865 AN: 2110

Alfa AF: 0.454 Hom.: 64939

Bravo AF: 0.361

Asia WGS AF: 0.317 AC: 1103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0040
DANN	Benign	0.28
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs971545; hg19: chr12-68591685;