2-238147187-G-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 24 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198582.4. 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
	KLHL30	NM_198582.4	MANE Select	c.1151-647G>T		intron	N/A	NP_940984.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLHL30	ENST00000409223.2	TSL:5 MANE Select	c.1151-647G>T		intron	N/A	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

African (AFR) AF: 0.948 AC: 39139 AN: 41298

American (AMR) AF: 0.818 AC: 12452 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.744 AC: 2582 AN: 3472

East Asian (EAS) AF: 0.894 AC: 4565 AN: 5106

South Asian (SAS) AF: 0.855 AC: 4090 AN: 4786

European-Finnish (FIN) AF: 0.831 AC: 8673 AN: 10434

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.755 AC: 51236 AN: 67842

Other (OTH) AF: 0.787 AC: 1649 AN: 2096

Alfa AF: 0.775 Hom.: 85071

Bravo AF: 0.831

Asia WGS AF: 0.885 AC: 3073 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.12
DANN	Benign	0.75
PhyloP100		-0.62
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7602358; hg19: chr2-239055828;