chr2-23408812-A-T

Variant names:

• chr2-23408812-A-T
• rs10495745
• NM_052920.2:c.-154+23032A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_052920.2(KLHL29):​c.-154+23032A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 152,074 control chromosomes in the GnomAD database, including 6,271 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 0.26 (6271 hom., cov: 32)
• Consequence: KLHL29 NM_052920.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0600
• Publications: 0 publications found

Genes affected

KLHL29 (HGNC:29404): (kelch like family member 29)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KLHL29	NM_052920.2	c.-154+23032A>T		intron_variant	Intron 1 of 13	ENST00000486442.6	NP_443152.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KLHL29	ENST00000486442.6	c.-154+23032A>T		intron_variant	Intron 1 of 13	5	NM_052920.2	ENSP00000420659.1

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39302 AN: 151956 Hom.: 6263 Cov.: 32

Gnomad AFR AF: 0.0739

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.259 AC: 39318 AN: 152074 Hom.: 6271 Cov.: 32 AF XY: 0.259 AC XY: 19240 AN XY: 74348

African (AFR) AF: 0.0737 AC: 3061 AN: 41518

American (AMR) AF: 0.342 AC: 5228 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 991 AN: 3472

East Asian (EAS) AF: 0.313 AC: 1617 AN: 5172

South Asian (SAS) AF: 0.340 AC: 1636 AN: 4812

European-Finnish (FIN) AF: 0.306 AC: 3234 AN: 10566

Middle Eastern (MID) AF: 0.192 AC: 56 AN: 292

European-Non Finnish (NFE) AF: 0.332 AC: 22542 AN: 67950

Other (OTH) AF: 0.268 AC: 565 AN: 2110

Alfa AF: 0.297 Hom.: 947

Bravo AF: 0.256

Asia WGS AF: 0.331 AC: 1153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.6
DANN	Benign	0.44
PhyloP100		-0.060
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: rs10495745; hg19: chr2-23631683;