chr12-10400668-G-A

Position:

• chr12-10400668-G-A

Variant summary

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

The NM_001199805.1(KLRC4-KLRK1):​c.-180-6801C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 151,742 control chromosomes in the GnomAD database, including 2,925 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 0.18 (2925 hom., cov: 31)
• Consequence: KLRC4-KLRK1 NM_001199805.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365

Genes affected

KLRC4-KLRK1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KLRC4-KLRK1	NM_001199805.1	c.-180-6801C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.184 AC: 27829 AN: 151624 Hom.: 2921 Cov.: 31

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.184 AC: 27856 AN: 151742 Hom.: 2925 Cov.: 31 AF XY: 0.187 AC XY: 13887 AN XY: 74132

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.334

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.175

Alfa AF: 0.161 Hom.: 1241

Bravo AF: 0.187

Asia WGS AF: 0.263 AC: 911 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.1
DANN	Benign	0.59

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

Publications

LitVar

Other links and lift over

dbSNP: rs728010; hg19: chr12-10553267;