rs12380505

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr9-21695894-A-C
• chr9-21695894-A-G
• chr9-21695894-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000427983.2(KHSRPP1):​n.719A>C 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 0.000000769 in 1,300,806 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 7.7e-7 (0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).

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>C		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000299739	ENST00000765951.1		n.106+10916A>C		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 7.69e-7 AC: 1 AN: 1300806 Hom.: 0 Cov.: 23 AF XY: 0.00000153 AC XY: 1 AN XY: 654686

African (AFR) AF: 0.00 AC: 0 AN: 30194

American (AMR) AF: 0.00 AC: 0 AN: 43732

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25110

East Asian (EAS) AF: 0.0000258 AC: 1 AN: 38774

South Asian (SAS) AF: 0.00 AC: 0 AN: 82544

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 52786

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5414

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 967360

Other (OTH) AF: 0.00 AC: 0 AN: 54892

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 54347

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	3.8
DANN	Benign	0.44
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;