rs543736

chr8-103000721-G-Achr8-103000721-G-C

Variant summary

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

The ENST00000659614.1(MAILR):n.2866G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 152,094 control chromosomes in the GnomAD database, including 11,749 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 0.38 (11749 hom., cov: 33)
• Consequence: MAILR ENST00000659614.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303

Genes affected

MAILR (HGNC:51558): (macrophage interferon regulatory lncRNA)

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 (AFR) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAILR	ENST00000659614.1	n.2866G>A		non_coding_transcript_exon_variant	6/6
MAILR	ENST00000520538.2	n.2633G>A		non_coding_transcript_exon_variant	5/5	3
MAILR	ENST00000520750.6	n.2915G>A		non_coding_transcript_exon_variant	7/7	5

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58341 AN: 151976 Hom.: 11724 Cov.: 33

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.384 AC: 58415 AN: 152094 Hom.: 11749 Cov.: 33 AF XY: 0.381 AC XY: 28319 AN XY: 74350

Gnomad4 AFR AF: 0.506

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.323

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.339

Alfa AF: 0.352 Hom.: 19934

Bravo AF: 0.390

Asia WGS AF: 0.316 AC: 1097 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	2.1
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs543736; hg19: chr8-104012949;