rs2246809

chr12-10404445-A-G

Variant summary

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

The NM_001199805.1(KLRC4-KLRK1):c.-181+3191T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.796 in 151,980 control chromosomes in the GnomAD database, including 48,256 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 0.80 (48256 hom., cov: 32)
• Consequence: KLRC4-KLRK1 NM_001199805.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52

Genes affected

KLRC4-KLRK1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.862 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KLRC4-KLRK1	NM_001199805.1	c.-181+3191T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.796 AC: 120879 AN: 151860 Hom.: 48213 Cov.: 32

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.767

Gnomad SAS AF: 0.885

Gnomad FIN AF: 0.810

Gnomad MID AF: 0.824

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.785

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

GnomAD4 genome AF: 0.796 AC: 120983 AN: 151980 Hom.: 48256 Cov.: 32 AF XY: 0.798 AC XY: 59265 AN XY: 74278

Gnomad4 AFR AF: 0.743

Gnomad4 AMR AF: 0.853

Gnomad4 ASJ AF: 0.803

Gnomad4 EAS AF: 0.768

Gnomad4 SAS AF: 0.884

Gnomad4 FIN AF: 0.810

Gnomad4 NFE AF: 0.810

Gnomad4 OTH AF: 0.787

Alfa AF: 0.799 Hom.: 7098

Bravo AF: 0.793

Asia WGS AF: 0.836 AC: 2894 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.40
Dann	Benign	0.36

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: rs2246809; hg19: chr12-10557044;