ENST00000630664.3:n.399+54678A>C

Variant names:

• chr4-155228962-A-C
• rs2880411
• ENST00000630664.3:n.399+54678A>C

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+54678A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,100 control chromosomes in the GnomAD database, including 2,159 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 0.16 (2159 hom., cov: 31)
• Consequence: MAP9-AS1 ENST00000630664.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.310
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.202 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+54678A>C		intron_variant	Intron 2 of 4	5

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24345 AN: 151982 Hom.: 2160 Cov.: 31

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.0925

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0519

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.160 AC: 24349 AN: 152100 Hom.: 2159 Cov.: 31 AF XY: 0.162 AC XY: 12056 AN XY: 74368

African (AFR) AF: 0.206 AC: 8536 AN: 41490

American (AMR) AF: 0.0924 AC: 1411 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 468 AN: 3468

East Asian (EAS) AF: 0.0518 AC: 268 AN: 5174

South Asian (SAS) AF: 0.166 AC: 798 AN: 4816

European-Finnish (FIN) AF: 0.201 AC: 2126 AN: 10572

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10150 AN: 67994

Other (OTH) AF: 0.140 AC: 296 AN: 2114

Alfa AF: 0.0941 Hom.: 152

Bravo AF: 0.151

Asia WGS AF: 0.154 AC: 537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	14
DANN	Benign	0.87
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs2880411; hg19: chr4-156150114;