rs9990860

chr4-155218913-A-G

Variant summary

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

The ENST00000630664.2(MAP9-AS1):n.208+44629A>G 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 0.238 in 152,060 control chromosomes in the GnomAD database, including 4,499 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 0.24 (4499 hom., cov: 32)
• Consequence: MAP9-AS1 ENST00000630664.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197

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 (AFR) allele frequency at 95% confidence interval = 0.303 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+44629A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36178 AN: 151940 Hom.: 4491 Cov.: 32

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.238 AC: 36196 AN: 152060 Hom.: 4499 Cov.: 32 AF XY: 0.234 AC XY: 17413 AN XY: 74332

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.199

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.240

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.231

Alfa AF: 0.244 Hom.: 559

Bravo AF: 0.234

Asia WGS AF: 0.186 AC: 647 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	4.0
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9990860; hg19: chr4-156140065;