2-169767711-C-T

Variant names:

• chr2-169767711-C-T
• rs2114646

Variant summary

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

The variant allele was found at a frequency of 0.232 in 373,276 control chromosomes in the GnomAD database, including 12,789 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 0.20 (3991 hom., cov: 32)
  • Exomes 𝑓: 0.25 (8798 hom.)
• Consequence: PTCHD3P2 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 11 publications found

Genes affected

PTCHD3P2 (HGNC:44946): (patched domain containing 3 pseudogene 2)

KLHL23 (HGNC:27506): (kelch like family member 23)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTCHD3P2		n.169767711C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KLHL23	ENST00000437875.1	c.830-5609C>T		intron_variant	Intron 2 of 2	3		ENSP00000394732.1
KLHL23	ENST00000448589.1	c.44-8730C>T		intron_variant	Intron 1 of 1	2		ENSP00000400833.1
PTCHD3P2	ENST00000424937.1	n.1087+2G>A		splice_donor_variant, intron_variant	Intron 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30277 AN: 151926 Hom.: 3979 Cov.: 32

Gnomad AFR AF: 0.0547

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.186

GnomAD4 exome AF: 0.255 AC: 56323 AN: 221232 Hom.: 8798 Cov.: 0 AF XY: 0.252 AC XY: 31720 AN XY: 125936

African (AFR) AF: 0.0518 AC: 343 AN: 6616

American (AMR) AF: 0.507 AC: 10472 AN: 20640

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 699 AN: 4630

East Asian (EAS) AF: 0.413 AC: 4047 AN: 9804

South Asian (SAS) AF: 0.294 AC: 10968 AN: 37308

European-Finnish (FIN) AF: 0.245 AC: 2584 AN: 10558

Middle Eastern (MID) AF: 0.133 AC: 261 AN: 1962

European-Non Finnish (NFE) AF: 0.207 AC: 24713 AN: 119448

Other (OTH) AF: 0.218 AC: 2236 AN: 10266

GnomAD4 genome AF: 0.199 AC: 30299 AN: 152044 Hom.: 3991 Cov.: 32 AF XY: 0.208 AC XY: 15456 AN XY: 74300

African (AFR) AF: 0.0548 AC: 2274 AN: 41516

American (AMR) AF: 0.354 AC: 5404 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 542 AN: 3470

East Asian (EAS) AF: 0.407 AC: 2099 AN: 5160

South Asian (SAS) AF: 0.319 AC: 1532 AN: 4806

European-Finnish (FIN) AF: 0.284 AC: 2997 AN: 10550

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.218 AC: 14788 AN: 67962

Other (OTH) AF: 0.186 AC: 392 AN: 2108

Alfa AF: 0.207 Hom.: 4612

Bravo AF: 0.199

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	16
DANN	Benign	0.86
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs2114646; hg19: chr2-170624221;