10-31679831-T-C

Variant names:

• chr10-31679831-T-C
• rs796126
• ENST00000775191.1:n.143+27475A>G

Variant summary

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

The ENST00000775191.1(MACORIS):​n.143+27475A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 152,058 control chromosomes in the GnomAD database, including 23,424 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 0.54 (23424 hom., cov: 33)
• Consequence: MACORIS ENST00000775191.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158
• Publications: 4 publications found

Genes affected

MACORIS (HGNC:53963): (macrophage enriched lincRNA repressor of IFN-gamma signaling)

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 = 0.698 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
MACORIS	ENST00000775191.1	n.143+27475A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.540 AC: 82002 AN: 151940 Hom.: 23421 Cov.: 33

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.663

Gnomad SAS AF: 0.719

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.539 AC: 82010 AN: 152058 Hom.: 23424 Cov.: 33 AF XY: 0.539 AC XY: 40106 AN XY: 74340

African (AFR) AF: 0.341 AC: 14143 AN: 41432

American (AMR) AF: 0.557 AC: 8511 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1879 AN: 3472

East Asian (EAS) AF: 0.664 AC: 3435 AN: 5176

South Asian (SAS) AF: 0.718 AC: 3458 AN: 4814

European-Finnish (FIN) AF: 0.517 AC: 5460 AN: 10564

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.635 AC: 43147 AN: 67998

Other (OTH) AF: 0.558 AC: 1178 AN: 2112

Alfa AF: 0.601 Hom.: 106037

Bravo AF: 0.526

Asia WGS AF: 0.653 AC: 2270 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.7
DANN	Benign	0.49
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs796126; hg19: chr10-31968759;