rs176614

Positions:

• chr6-62238689-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_152688.4(KHDRBS2):​c.91+47169G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.41 (2379 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: KHDRBS2 NM_152688.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.159

Genes affected

KHDRBS2 (HGNC:18114): (KH RNA binding domain containing, signal transduction associated 2) Predicted to enable mRNA binding activity and poly(A) binding activity. Predicted to be involved in regulation of alternative mRNA splicing, via spliceosome. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KHDRBS2	NM_152688.4	c.91+47169G>A		intron_variant		ENST00000281156.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KHDRBS2	ENST00000281156.5	c.91+47169G>A		intron_variant		1	NM_152688.4	P1
KHDRBS2	ENST00000675091.1	c.91+47169G>A		intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00 AC: 25191 AN: 60958 Hom.: 2375 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.508

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.413

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.413 AC: 25214 AN: 61034 Hom.: 2379 Cov.: 0 AF XY: 0.412 AC XY: 12187 AN XY: 29574

Gnomad4 AFR AF: 0.448

Gnomad4 AMR AF: 0.336

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.415

Alfa AF: 0.183 Hom.: 215

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.099

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs176614; hg19: chr6-62948594;