rs7873355

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000413804.2. 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
	JKAMPP1	ENST00000413804.2	TSL:6	n.878G>C		non_coding_transcript_exon	Exon 1 of 1

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 v4.9

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

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

Other links and lift over

dbSNP: rs7873355;

hg19: chr9-12288197;