9-21695894-A-G

Position:

• chr9-21695894-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

KHSRPP1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KHSRPP1		n.21695894A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KHSRPP1	ENST00000427983.2	n.719A>G		non_coding_transcript_exon_variant	1/1	6

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

Gnomad4 AFR exome AF: 0.823

Gnomad4 AMR exome AF: 0.459

Gnomad4 ASJ exome AF: 0.571

Gnomad4 EAS exome AF: 0.634

Gnomad4 SAS exome AF: 0.423

Gnomad4 FIN exome AF: 0.566

Gnomad4 NFE exome AF: 0.531

Gnomad4 OTH exome AF: 0.550

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

Gnomad4 AFR AF: 0.809

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.577

Gnomad4 EAS AF: 0.701

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.533

Gnomad4 OTH AF: 0.590

Alfa AF: 0.527 Hom.: 33489

Bravo AF: 0.619

Asia WGS AF: 0.536 AC: 1862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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