ENST00000630664.3:n.400-84003C>T

Variant names:

• chr4-155270206-C-T
• rs10517607
• ENST00000630664.3:n.400-84003C>T

Variant summary

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

The ENST00000630664.3(MAP9-AS1):​n.400-84003C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 151,660 control chromosomes in the GnomAD database, including 2,630 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 (2630 hom., cov: 32)
• Consequence: MAP9-AS1 ENST00000630664.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.242
• Publications: 1 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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.262 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.400-84003C>T		intron_variant	Intron 2 of 4	5

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25013 AN: 151542 Hom.: 2632 Cov.: 32

Gnomad AFR AF: 0.0466

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.165 AC: 25013 AN: 151660 Hom.: 2630 Cov.: 32 AF XY: 0.174 AC XY: 12904 AN XY: 74072

African (AFR) AF: 0.0466 AC: 1933 AN: 41480

American (AMR) AF: 0.139 AC: 2107 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 537 AN: 3468

East Asian (EAS) AF: 0.206 AC: 1056 AN: 5116

South Asian (SAS) AF: 0.274 AC: 1320 AN: 4820

European-Finnish (FIN) AF: 0.321 AC: 3384 AN: 10552

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14084 AN: 67748

Other (OTH) AF: 0.130 AC: 274 AN: 2102

Alfa AF: 0.187 Hom.: 462

Bravo AF: 0.142

Asia WGS AF: 0.237 AC: 822 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.6
DANN	Benign	0.68
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs10517607; hg19: chr4-156191358;