chr8-103000721-G-A

Variant names:

• chr8-103000721-G-A
• rs543736
• ENST00000520538.2:n.2633G>A

Variant summary

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

The ENST00000520538.2(MAILR):​n.2633G>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 ENST00000520538.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303
• Publications: 9 publications found

Genes affected

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

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 (AFR) allele frequency at 95% confidence interval = 0.5 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
MAILR	ENST00000520538.2	n.2633G>A		non_coding_transcript_exon_variant	Exon 5 of 5	3
MAILR	ENST00000520750.6	n.2915G>A		non_coding_transcript_exon_variant	Exon 7 of 7	5
MAILR	ENST00000659614.1	n.2866G>A		non_coding_transcript_exon_variant	Exon 6 of 6
MAILR	ENST00000849071.1	n.971G>A		non_coding_transcript_exon_variant	Exon 3 of 3

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

African (AFR) AF: 0.506 AC: 20973 AN: 41456

American (AMR) AF: 0.321 AC: 4902 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 941 AN: 3470

East Asian (EAS) AF: 0.311 AC: 1610 AN: 5176

South Asian (SAS) AF: 0.329 AC: 1587 AN: 4820

European-Finnish (FIN) AF: 0.323 AC: 3412 AN: 10566

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23882 AN: 68004

Other (OTH) AF: 0.339 AC: 717 AN: 2116

Alfa AF: 0.358 Hom.: 43197

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
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs543736; hg19: chr8-104012949;