6-97010244-G-GAAGC

Position:

• chr6-97010244-G-GAAGC

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000620278.1(KLHL32):​c.-653_-652insAGCA variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.65 (33894 hom., cov: 0)
  • Exomes 𝑓: 0.70 (5 hom.)
• Consequence: KLHL32 ENST00000620278.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

KLHL32 (HGNC:21221): (kelch like family member 32)

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.883 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KLHL32	NM_052904.4	c.205-31247_205-31246insAGCA		intron_variant		ENST00000369261.9	NP_443136.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KLHL32	ENST00000369261.9	c.205-31247_205-31246insAGCA		intron_variant		2	NM_052904.4	ENSP00000358265	P1

Frequencies

GnomAD3 genomes AF: 0.650 AC: 98384 AN: 151358 Hom.: 33834 Cov.: 0

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.483

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.636

GnomAD4 exome AF: 0.700 AC: 14 AN: 20 Hom.: 5 Cov.: 0 AF XY: 0.667 AC XY: 12 AN XY: 18

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.833

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.650 AC: 98505 AN: 151474 Hom.: 33894 Cov.: 0 AF XY: 0.651 AC XY: 48175 AN XY: 73960

Gnomad4 AFR AF: 0.890

Gnomad4 AMR AF: 0.672

Gnomad4 ASJ AF: 0.577

Gnomad4 EAS AF: 0.600

Gnomad4 SAS AF: 0.696

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.636

Alfa AF: 0.572 Hom.: 2737

Asia WGS AF: 0.701 AC: 2439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2307652; hg19: chr6-97458120;