rs796158

Variant names:

• chr10-31693864-T-G
• rs796158
• ENST00000433770.4:n.297-517A>C

Variant summary

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

The ENST00000433770.4(MACORIS):​n.297-517A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 151,928 control chromosomes in the GnomAD database, including 14,245 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 0.42 (14245 hom., cov: 31)
• Consequence: MACORIS ENST00000433770.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.361
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.549 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MACORIS	NR_184023.1	n.143-517A>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MACORIS	ENST00000433770.4	n.297-517A>C		intron_variant	Intron 1 of 1	2
MACORIS	ENST00000775191.1	n.143+13442A>C		intron_variant	Intron 1 of 1
MACORIS	ENST00000775192.1	n.166-517A>C		intron_variant	Intron 2 of 2
MACORIS	ENST00000775193.1	n.87-517A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64070 AN: 151810 Hom.: 14249 Cov.: 31

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.422 AC: 64073 AN: 151928 Hom.: 14245 Cov.: 31 AF XY: 0.422 AC XY: 31314 AN XY: 74262

African (AFR) AF: 0.263 AC: 10916 AN: 41434

American (AMR) AF: 0.463 AC: 7075 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1332 AN: 3468

East Asian (EAS) AF: 0.487 AC: 2516 AN: 5170

South Asian (SAS) AF: 0.567 AC: 2722 AN: 4802

European-Finnish (FIN) AF: 0.400 AC: 4220 AN: 10542

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33743 AN: 67934

Other (OTH) AF: 0.435 AC: 917 AN: 2106

Alfa AF: 0.447 Hom.: 1940

Bravo AF: 0.417

Asia WGS AF: 0.502 AC: 1745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.7
DANN	Benign	0.67
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs796158; hg19: chr10-31982792;