rs2870951

Variant names:

• chr12-68190765-A-G
• rs2870951
• ENST00000536914.1:n.337-43764A>G

Your query was ambiguous. Multiple possible variants found:

• chr12-68190765-A-G
• chr12-68190765-A-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+4821A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 152,104 control chromosomes in the GnomAD database, including 18,644 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 0.48 (18644 hom., cov: 32)
• Consequence: LOC105369818 XR_001749193.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369818	XR_001749193.2	n.3040+4821A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFNG-AS1	ENST00000536914.1	n.337-43764A>G		intron_variant	Intron 5 of 5	5

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72241 AN: 151986 Hom.: 18632 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.475 AC: 72276 AN: 152104 Hom.: 18644 Cov.: 32 AF XY: 0.464 AC XY: 34485 AN XY: 74352

African (AFR) AF: 0.322 AC: 13352 AN: 41508

American (AMR) AF: 0.422 AC: 6442 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2122 AN: 3470

East Asian (EAS) AF: 0.152 AC: 789 AN: 5188

South Asian (SAS) AF: 0.402 AC: 1938 AN: 4824

European-Finnish (FIN) AF: 0.446 AC: 4700 AN: 10546

Middle Eastern (MID) AF: 0.674 AC: 194 AN: 288

European-Non Finnish (NFE) AF: 0.604 AC: 41081 AN: 67978

Other (OTH) AF: 0.517 AC: 1092 AN: 2112

Alfa AF: 0.545 Hom.: 10458

Bravo AF: 0.465

Asia WGS AF: 0.350 AC: 1218 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	0.16
DANN	Benign	0.46
PhyloP100		-0.45

Splicing

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

Publications

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Other links and lift over

dbSNP: rs2870951; hg19: chr12-68584545;