4-155220960-T-G

Variant names:

• chr4-155220960-T-G
• rs2342652
• ENST00000630664.3:n.399+46676T>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+46676T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 152,108 control chromosomes in the GnomAD database, including 33,041 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 0.64 (33041 hom., cov: 32)
• Consequence: MAP9-AS1 ENST00000630664.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.129
• Publications: 3 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000630664.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAP9-AS1	ENST00000630664.3	TSL:5	n.399+46676T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.642 AC: 97642 AN: 151990 Hom.: 32998 Cov.: 32

Gnomad AFR AF: 0.852

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.643 AC: 97741 AN: 152108 Hom.: 33041 Cov.: 32 AF XY: 0.644 AC XY: 47881 AN XY: 74340

African (AFR) AF: 0.852 AC: 35363 AN: 41522

American (AMR) AF: 0.519 AC: 7922 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1745 AN: 3470

East Asian (EAS) AF: 0.796 AC: 4109 AN: 5164

South Asian (SAS) AF: 0.573 AC: 2765 AN: 4822

European-Finnish (FIN) AF: 0.627 AC: 6635 AN: 10578

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.547 AC: 37148 AN: 67972

Other (OTH) AF: 0.603 AC: 1273 AN: 2112

Alfa AF: 0.580 Hom.: 21315

Bravo AF: 0.641

Asia WGS AF: 0.720 AC: 2504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.8
DANN	Benign	0.59
PhyloP100		0.13

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2342652;

hg19: chr4-156142112;