rs7081678

Variant names:

• chr10-31701695-G-A
• rs7081678
• ENST00000433770.4:n.296+5611C>T

Variant summary

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

The ENST00000433770.4(MACORIS):​n.296+5611C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0611 in 152,248 control chromosomes in the GnomAD database, including 325 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 0.061 (325 hom., cov: 32)
• Consequence: MACORIS ENST00000433770.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 14 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0939 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MACORIS	NR_184023.1	n.142+5611C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MACORIS	ENST00000433770.4	n.296+5611C>T		intron_variant	Intron 1 of 1	2
MACORIS	ENST00000775191.1	n.143+5611C>T		intron_variant	Intron 1 of 1
MACORIS	ENST00000775192.1	n.165+5611C>T		intron_variant	Intron 2 of 2
MACORIS	ENST00000775193.1	n.86+399C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0610 AC: 9286 AN: 152130 Hom.: 326 Cov.: 32

Gnomad AFR AF: 0.0304

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.0981

Gnomad ASJ AF: 0.0608

Gnomad EAS AF: 0.0214

Gnomad SAS AF: 0.0252

Gnomad FIN AF: 0.0789

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0737

Gnomad OTH AF: 0.0623

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

GnomAD4 genome AF: 0.0611 AC: 9298 AN: 152248 Hom.: 325 Cov.: 32 AF XY: 0.0613 AC XY: 4567 AN XY: 74446

African (AFR) AF: 0.0305 AC: 1269 AN: 41556

American (AMR) AF: 0.0980 AC: 1499 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0608 AC: 211 AN: 3468

East Asian (EAS) AF: 0.0211 AC: 109 AN: 5178

South Asian (SAS) AF: 0.0257 AC: 124 AN: 4830

European-Finnish (FIN) AF: 0.0789 AC: 836 AN: 10602

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0737 AC: 5015 AN: 68008

Other (OTH) AF: 0.0621 AC: 131 AN: 2110

Alfa AF: 0.0728 Hom.: 669

Bravo AF: 0.0635

Asia WGS AF: 0.0240 AC: 84 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.095
DANN	Benign	0.49
PhyloP100		-1.9
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs7081678; hg19: chr10-31990623;