rs952108

Variant names:

• chr19-51008674-G-A
• rs952108
• NM_012315.2:c.200+509C>T

Your query was ambiguous. Multiple possible variants found:

• chr19-51008674-G-A
• chr19-51008674-G-T

Variant summary

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

The NM_012315.2(KLK9):​c.200+509C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 152,042 control chromosomes in the GnomAD database, including 24,036 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 0.54 (24036 hom., cov: 33)
• Consequence: KLK9 NM_012315.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.502
• Publications: 6 publications found

Genes affected

KLK9 (HGNC:6370): (kallikrein related peptidase 9) The protein encoded by this gene is a kallikrein-related serine protease. This gene is activated by steroid hormones in a human breast cancer cell line, making it a good marker for cancer detection. The encoded protein is found primarily in the cytoplasm.[provided by RefSeq, Oct 2010]

ENSG00000269741 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KLK9	NM_012315.2	c.200+509C>T		intron_variant	Intron 2 of 4	ENST00000594211.2	NP_036447.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KLK9	ENST00000594211.2	c.200+509C>T		intron_variant	Intron 2 of 4	1	NM_012315.2	ENSP00000469417.1
ENSG00000269741	ENST00000250366.6	n.200+509C>T		intron_variant	Intron 2 of 6	2		ENSP00000250366.5
KLK9	ENST00000544410.1	n.43+831C>T		intron_variant	Intron 1 of 3	2		ENSP00000443289.1
ENSG00000267879	ENST00000594512.1	n.430-3349G>A		intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81485 AN: 151924 Hom.: 24000 Cov.: 33

Gnomad AFR AF: 0.793

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.515

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

GnomAD4 genome AF: 0.537 AC: 81571 AN: 152042 Hom.: 24036 Cov.: 33 AF XY: 0.527 AC XY: 39173 AN XY: 74312

African (AFR) AF: 0.793 AC: 32909 AN: 41510

American (AMR) AF: 0.539 AC: 8220 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1448 AN: 3466

East Asian (EAS) AF: 0.360 AC: 1865 AN: 5180

South Asian (SAS) AF: 0.327 AC: 1575 AN: 4812

European-Finnish (FIN) AF: 0.360 AC: 3799 AN: 10548

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.443 AC: 30083 AN: 67952

Other (OTH) AF: 0.509 AC: 1074 AN: 2108

Alfa AF: 0.531 Hom.: 3298

Bravo AF: 0.563

Asia WGS AF: 0.329 AC: 1143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.5
DANN	Benign	0.48
PhyloP100		0.50
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs952108; hg19: chr19-51511930;