ENST00000427983.2:n.719A>G

Variant names:

• chr9-21695894-A-G
• rs12380505
• ENST00000427983.2:n.719A>G

Variant summary

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

The ENST00000427983.2(KHSRPP1):​n.719A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.542 in 1,451,122 control chromosomes in the GnomAD database, including 218,070 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 0.61 (29528 hom., cov: 32)
  • Exomes 𝑓: 0.53 (188542 hom.)
• Consequence: KHSRPP1 ENST00000427983.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.67
• Publications: 7 publications found

Genes affected

KHSRPP1 (HGNC:39198): (KH-type splicing regulatory protein pseudogene 1)

ENSG00000299739 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000427983.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KHSRPP1	ENST00000427983.2	TSL:6	n.719A>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000299739	ENST00000765951.1		n.106+10916A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92644 AN: 151812 Hom.: 29511 Cov.: 32

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.589

GnomAD4 exome AF: 0.534 AC: 694298 AN: 1299192 Hom.: 188542 Cov.: 23 AF XY: 0.530 AC XY: 346338 AN XY: 653890

African (AFR) AF: 0.823 AC: 24825 AN: 30182

American (AMR) AF: 0.459 AC: 20076 AN: 43716

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 14328 AN: 25102

East Asian (EAS) AF: 0.634 AC: 24597 AN: 38768

South Asian (SAS) AF: 0.423 AC: 34931 AN: 82514

European-Finnish (FIN) AF: 0.566 AC: 29855 AN: 52774

Middle Eastern (MID) AF: 0.518 AC: 2804 AN: 5408

European-Non Finnish (NFE) AF: 0.531 AC: 512744 AN: 965882

Other (OTH) AF: 0.550 AC: 30138 AN: 54846

GnomAD4 genome AF: 0.610 AC: 92714 AN: 151930 Hom.: 29528 Cov.: 32 AF XY: 0.606 AC XY: 44964 AN XY: 74204

African (AFR) AF: 0.809 AC: 33552 AN: 41466

American (AMR) AF: 0.507 AC: 7749 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.577 AC: 2002 AN: 3470

East Asian (EAS) AF: 0.701 AC: 3609 AN: 5146

South Asian (SAS) AF: 0.441 AC: 2121 AN: 4808

European-Finnish (FIN) AF: 0.543 AC: 5729 AN: 10546

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.533 AC: 36173 AN: 67900

Other (OTH) AF: 0.590 AC: 1248 AN: 2114

Alfa AF: 0.537 Hom.: 54347

Bravo AF: 0.619

Asia WGS AF: 0.536 AC: 1862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	4.3
DANN	Benign	0.37
PhyloP100		2.7

Splicing

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

Other links and lift over

dbSNP: rs12380505; hg19: chr9-21695893; COSMIC: COSV70238375;