rs7972757

chr12-10393541-A-Gchr12-10393541-A-T

Variant summary

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

The NM_001199805.1(KLRC4-KLRK1):c.-123+269T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,178 control chromosomes in the GnomAD database, including 1,860 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 0.15 (1860 hom., cov: 32)
• Consequence: KLRC4-KLRK1 NM_001199805.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112

Genes affected

KLRC4-KLRK1 (HGNC:):

KLRK1-AS1 (HGNC:54868): (KLRK1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KLRC4-KLRK1	NM_001199805.1	c.-123+269T>C		intron_variant
KLRK1-AS1	NR_120430.1	n.503-2638A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KLRK1-AS1	ENST00000500682.1	n.503-2638A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22324 AN: 152060 Hom.: 1857 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.147 AC: 22347 AN: 152178 Hom.: 1860 Cov.: 32 AF XY: 0.151 AC XY: 11273 AN XY: 74414

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.197

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.147

Alfa AF: 0.129 Hom.: 754

Bravo AF: 0.149

Asia WGS AF: 0.256 AC: 887 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.8
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: rs7972757; hg19: chr12-10546140;