rs17304901

Positions:

• chr4-155217220-G-A

Variant summary

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

The ENST00000630664.2(MAP9-AS1):​n.208+42936G>A 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 0.193 in 152,612 control chromosomes in the GnomAD database, including 3,587 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 0.19 (3577 hom., cov: 32)
  • Exomes 𝑓: 0.19 (10 hom.)
• Consequence: MAP9-AS1 ENST00000630664.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.821

Genes affected

MAP9-AS1 (HGNC:56110): (MAP9 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.263 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
MAP9-AS1	ENST00000630664.2	n.208+42936G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29330 AN: 151960 Hom.: 3575 Cov.: 32

Gnomad AFR AF: 0.0609

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.0533

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.233

GnomAD4 exome AF: 0.191 AC: 102 AN: 534 Hom.: 10 AF XY: 0.195 AC XY: 66 AN XY: 338

Gnomad4 FIN exome AF: 0.188

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.125

GnomAD4 genome AF: 0.193 AC: 29335 AN: 152078 Hom.: 3577 Cov.: 32 AF XY: 0.191 AC XY: 14229 AN XY: 74328

Gnomad4 AFR AF: 0.0607

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.0539

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.230

Alfa AF: 0.257 Hom.: 5527

Bravo AF: 0.192

Asia WGS AF: 0.118 AC: 410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.33
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17304901; hg19: chr4-156138372;