ENST00000460528.1:n.1162-1806A>G

Variant names:

• chr7-128876416-T-C
• rs13238831
• ENST00000460528.1:n.1162-1806A>G

Variant summary

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

The ENST00000460528.1(KCP):​n.1162-1806A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 152,042 control chromosomes in the GnomAD database, including 4,871 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 0.22 (4871 hom., cov: 32)
• Consequence: KCP ENST00000460528.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.48
• Publications: 7 publications found

Genes affected

KCP (HGNC:17585): (kielin cysteine rich BMP regulator) Predicted to act upstream of or within hematopoietic progenitor cell differentiation and positive regulation of BMP signaling pathway. Predicted to be located in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KCP	ENST00000460528.1	n.1162-1806A>G		intron_variant	Intron 2 of 3	2
KCP	ENST00000492679.5	n.1001-1806A>G		intron_variant	Intron 6 of 9	2
KCP	ENST00000676619.1	n.571-1806A>G		intron_variant	Intron 4 of 10

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33863 AN: 151924 Hom.: 4849 Cov.: 32

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.223 AC: 33930 AN: 152042 Hom.: 4871 Cov.: 32 AF XY: 0.222 AC XY: 16540 AN XY: 74338

African (AFR) AF: 0.374 AC: 15469 AN: 41398

American (AMR) AF: 0.204 AC: 3125 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 475 AN: 3472

East Asian (EAS) AF: 0.438 AC: 2260 AN: 5160

South Asian (SAS) AF: 0.204 AC: 983 AN: 4828

European-Finnish (FIN) AF: 0.134 AC: 1424 AN: 10598

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9658 AN: 67976

Other (OTH) AF: 0.220 AC: 464 AN: 2110

Alfa AF: 0.141 Hom.: 1018

Bravo AF: 0.240

Asia WGS AF: 0.323 AC: 1121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.16
DANN	Benign	0.29
PhyloP100		-3.5

Splicing

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

Other links and lift over

dbSNP: rs13238831; hg19: chr7-128516470;