rs7081678

chr10-31701695-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_184023.1(MACORIS):n.142+5611C>T variant causes a intron, non coding transcript 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 NR_184023.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
MACORIS	NR_184023.1	n.142+5611C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MACORIS	ENST00000433770.3	n.142+5611C>T		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.0305

Gnomad4 AMR AF: 0.0980

Gnomad4 ASJ AF: 0.0608

Gnomad4 EAS AF: 0.0211

Gnomad4 SAS AF: 0.0257

Gnomad4 FIN AF: 0.0789

Gnomad4 NFE AF: 0.0737

Gnomad4 OTH AF: 0.0621

Alfa AF: 0.0722 Hom.: 443

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7081678; hg19: chr10-31990623;