rs13238831

Positions:

• chr7-128876416-T-C
• chr7-128876416-T-G

Variant summary

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

The ENST00000678888.1(KCP):​c.380-1806A>G variant causes a intron, NMD transcript 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 ENST00000678888.1 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.48

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KCP	ENST00000678888.1	c.380-1806A>G		intron_variant, NMD_transcript_variant
KCP	ENST00000460528.1	n.1162-1806A>G		intron_variant, non_coding_transcript_variant		2
KCP	ENST00000492679.5	n.1001-1806A>G		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.374

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.438

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.220

Alfa AF: 0.139 Hom.: 931

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13238831; hg19: chr7-128516470;