rs722748

Variant names:

• chr12-68106744-G-A
• rs722748
• ENST00000536914.1:n.336+80036G>A

Variant summary

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

The ENST00000777404.1(ENSG00000301254):​n.168-10773C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 152,108 control chromosomes in the GnomAD database, including 13,231 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 0.40 (13231 hom., cov: 32)
• Consequence: ENSG00000301254 ENST00000777404.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.471
• Publications: 7 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000777404.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFNG-AS1	ENST00000536914.1	TSL:5	n.336+80036G>A		intron	N/A
	ENSG00000301254	ENST00000777404.1		n.168-10773C>T		intron	N/A
	ENSG00000301254	ENST00000777405.1		n.188-10773C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61550 AN: 151990 Hom.: 13218 Cov.: 32

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.405 AC: 61596 AN: 152108 Hom.: 13231 Cov.: 32 AF XY: 0.395 AC XY: 29400 AN XY: 74348

African (AFR) AF: 0.522 AC: 21641 AN: 41494

American (AMR) AF: 0.294 AC: 4490 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1215 AN: 3470

East Asian (EAS) AF: 0.108 AC: 561 AN: 5184

South Asian (SAS) AF: 0.186 AC: 899 AN: 4824

European-Finnish (FIN) AF: 0.383 AC: 4047 AN: 10556

Middle Eastern (MID) AF: 0.360 AC: 105 AN: 292

European-Non Finnish (NFE) AF: 0.405 AC: 27526 AN: 67988

Other (OTH) AF: 0.401 AC: 844 AN: 2106

Alfa AF: 0.415 Hom.: 1711

Bravo AF: 0.404

Asia WGS AF: 0.202 AC: 706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.2
DANN	Benign	0.36
PhyloP100		0.47

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs722748;

hg19: chr12-68500524;