chr9-12287871-G-C

Variant names:

• chr9-12287871-G-C
• rs1416582
• ENST00000413804.2:n.552G>C

Variant summary

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

The ENST00000413804.2(JKAMPP1):​n.552G>C variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.258 in 214,152 control chromosomes in the GnomAD database, including 7,610 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 0.28 (6121 hom., cov: 31)
  • Exomes 𝑓: 0.20 (1489 hom.)
• Consequence: JKAMPP1 ENST00000413804.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.39
• Publications: 4 publications found

Genes affected

JKAMPP1 (HGNC:49759): (JNK1/MAPK8-associated membrane protein pseudogene 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
JKAMPP1		n.12287871G>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
JKAMPP1	ENST00000413804.2	n.552G>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42444 AN: 151616 Hom.: 6117 Cov.: 31

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.270

GnomAD4 exome AF: 0.204 AC: 12738 AN: 62418 Hom.: 1489 Cov.: 0 AF XY: 0.206 AC XY: 6998 AN XY: 33984

African (AFR) AF: 0.275 AC: 322 AN: 1170

American (AMR) AF: 0.318 AC: 809 AN: 2542

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 176 AN: 854

East Asian (EAS) AF: 0.323 AC: 772 AN: 2390

South Asian (SAS) AF: 0.267 AC: 2132 AN: 7984

European-Finnish (FIN) AF: 0.147 AC: 1783 AN: 12110

Middle Eastern (MID) AF: 0.283 AC: 511 AN: 1808

European-Non Finnish (NFE) AF: 0.185 AC: 5636 AN: 30462

Other (OTH) AF: 0.193 AC: 597 AN: 3098

GnomAD4 genome AF: 0.280 AC: 42483 AN: 151734 Hom.: 6121 Cov.: 31 AF XY: 0.279 AC XY: 20664 AN XY: 74112

African (AFR) AF: 0.300 AC: 12406 AN: 41370

American (AMR) AF: 0.343 AC: 5218 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1117 AN: 3466

East Asian (EAS) AF: 0.362 AC: 1856 AN: 5134

South Asian (SAS) AF: 0.339 AC: 1626 AN: 4798

European-Finnish (FIN) AF: 0.189 AC: 1982 AN: 10488

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17408 AN: 67940

Other (OTH) AF: 0.272 AC: 573 AN: 2104

Alfa AF: 0.261 Hom.: 638

Bravo AF: 0.294

Asia WGS AF: 0.346 AC: 1205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	14
DANN	Benign	0.75
PhyloP100		6.4

Splicing

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

Other links and lift over

dbSNP: rs1416582; hg19: chr9-12287871;