2-238147187-G-T

Variant names:

• chr2-238147187-G-T
• rs7602358
• NM_198582.4:c.1151-647G>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_198582.4(KLHL30):​c.1151-647G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.827 in 151,456 control chromosomes in the GnomAD database, including 52,290 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 0.83 (52290 hom., cov: 27)
• Consequence: KLHL30 NM_198582.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.623

Genes affected

KLHL30 (HGNC:24770): (kelch like family member 30)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.94 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KLHL30	NM_198582.4	c.1151-647G>T		intron_variant	Intron 5 of 7	ENST00000409223.2	NP_940984.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KLHL30	ENST00000409223.2	c.1151-647G>T		intron_variant	Intron 5 of 7	5	NM_198582.4	ENSP00000386389.1

Frequencies

GnomAD3 genomes AF: 0.827 AC: 125150 AN: 151340 Hom.: 52229 Cov.: 27

Gnomad AFR AF: 0.948

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.818

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.894

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.720

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.786

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

GnomAD4 genome AF: 0.827 AC: 125268 AN: 151456 Hom.: 52290 Cov.: 27 AF XY: 0.831 AC XY: 61482 AN XY: 73966

Gnomad4 AFR AF: 0.948

Gnomad4 AMR AF: 0.818

Gnomad4 ASJ AF: 0.744

Gnomad4 EAS AF: 0.894

Gnomad4 SAS AF: 0.855

Gnomad4 FIN AF: 0.831

Gnomad4 NFE AF: 0.755

Gnomad4 OTH AF: 0.787

Alfa AF: 0.767 Hom.: 60431

Bravo AF: 0.831

Asia WGS AF: 0.885 AC: 3073 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.12
DANN	Benign	0.75

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: rs7602358; hg19: chr2-239055828;