9-12288197-G-C

Variant names:

• chr9-12288197-G-C
• rs7873355
• ENST00000413804.2:n.878G>C

Variant summary

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

The ENST00000413804.2(JKAMPP1):​n.878G>C variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.421 in 162,442 control chromosomes in the GnomAD database, including 14,772 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 0.43 (14227 hom., cov: 32)
  • Exomes 𝑓: 0.31 (545 hom.)
• Consequence: JKAMPP1 ENST00000413804.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.97
• Publications: 2 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=-0.55).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
JKAMPP1		n.12288197G>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
JKAMPP1	ENST00000413804.2	n.878G>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65127 AN: 151740 Hom.: 14217 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.438

GnomAD4 exome AF: 0.309 AC: 3271 AN: 10582 Hom.: 545 Cov.: 0 AF XY: 0.311 AC XY: 1902 AN XY: 6106

African (AFR) AF: 0.502 AC: 246 AN: 490

American (AMR) AF: 0.234 AC: 72 AN: 308

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 51 AN: 100

East Asian (EAS) AF: 0.339 AC: 241 AN: 710

South Asian (SAS) AF: 0.387 AC: 425 AN: 1098

European-Finnish (FIN) AF: 0.248 AC: 446 AN: 1796

Middle Eastern (MID) AF: 0.405 AC: 497 AN: 1226

European-Non Finnish (NFE) AF: 0.263 AC: 1145 AN: 4346

Other (OTH) AF: 0.291 AC: 148 AN: 508

GnomAD4 genome AF: 0.429 AC: 65185 AN: 151860 Hom.: 14227 Cov.: 32 AF XY: 0.425 AC XY: 31547 AN XY: 74214

African (AFR) AF: 0.466 AC: 19300 AN: 41428

American (AMR) AF: 0.471 AC: 7181 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2042 AN: 3458

East Asian (EAS) AF: 0.478 AC: 2451 AN: 5128

South Asian (SAS) AF: 0.489 AC: 2358 AN: 4820

European-Finnish (FIN) AF: 0.276 AC: 2902 AN: 10522

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.407 AC: 27628 AN: 67940

Other (OTH) AF: 0.438 AC: 924 AN: 2110

Alfa AF: 0.406 Hom.: 1619

Bravo AF: 0.445

Asia WGS AF: 0.472 AC: 1643 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	15
DANN	Benign	0.58
PhyloP100		6.0

Splicing

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

Other links and lift over

dbSNP: rs7873355; hg19: chr9-12288197;