rs9990860

Variant names:

• chr4-155218913-A-G
• rs9990860
• ENST00000630664.3:n.399+44629A>G

Variant summary

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

The ENST00000630664.3(MAP9-AS1):​n.399+44629A>G variant causes a intron 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 ENST00000630664.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAP9-AS1	ENST00000630664.3	n.399+44629A>G		intron_variant	Intron 2 of 4	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

African (AFR) AF: 0.307 AC: 12742 AN: 41500

American (AMR) AF: 0.148 AC: 2262 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 678 AN: 3466

East Asian (EAS) AF: 0.199 AC: 1029 AN: 5182

South Asian (SAS) AF: 0.178 AC: 857 AN: 4824

European-Finnish (FIN) AF: 0.240 AC: 2537 AN: 10582

Middle Eastern (MID) AF: 0.216 AC: 63 AN: 292

European-Non Finnish (NFE) AF: 0.225 AC: 15308 AN: 67954

Other (OTH) AF: 0.231 AC: 486 AN: 2108

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
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs9990860; hg19: chr4-156140065;