18-63909374-C-T

Position:

• chr18-63909374-C-T

Variant summary

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

The NM_005024.3(SERPINB10):​c.-10+1334C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0492 in 151,894 control chromosomes in the GnomAD database, including 376 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 0.049 (376 hom., cov: 32)
• Consequence: SERPINB10 NM_005024.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497

Genes affected

SERPINB10 (HGNC:8942): (serpin family B member 10) This gene is a member of the serpin peptidase inhibitor, clade B family and is found in a cluster of other similar genes on chromosome 18. The protein encoded by this gene appears to help control the regulation of protease functions during hematopoiesis. Variations in this gene may increase the risk of prostate cancer. [provided by RefSeq, Dec 2015]

ENSG00000289724 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SERPINB10	NM_005024.3	c.-10+1334C>T		intron_variant		ENST00000238508.8	NP_005015.1
SERPINB10	XM_011526027.2	c.-83-823C>T		intron_variant			XP_011524329.1
SERPINB10	XM_017025793.2	c.-10+1334C>T		intron_variant			XP_016881282.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SERPINB10	ENST00000238508.8	c.-10+1334C>T		intron_variant		1	NM_005024.3	ENSP00000238508.3
ENSG00000289724	ENST00000397996.6	c.627+1334C>T		intron_variant		5		ENSP00000381082.2
ENSG00000289724	ENST00000418725.1	c.547-6128C>T		intron_variant		5		ENSP00000392381.1

Frequencies

GnomAD3 genomes AF: 0.0492 AC: 7467 AN: 151776 Hom.: 374 Cov.: 32

Gnomad AFR AF: 0.0897

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0499

Gnomad ASJ AF: 0.0127

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.0830

Gnomad FIN AF: 0.0230

Gnomad MID AF: 0.0478

Gnomad NFE AF: 0.0153

Gnomad OTH AF: 0.0517

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

GnomAD4 genome AF: 0.0492 AC: 7474 AN: 151894 Hom.: 376 Cov.: 32 AF XY: 0.0505 AC XY: 3745 AN XY: 74220

Gnomad4 AFR AF: 0.0895

Gnomad4 AMR AF: 0.0499

Gnomad4 ASJ AF: 0.0127

Gnomad4 EAS AF: 0.221

Gnomad4 SAS AF: 0.0822

Gnomad4 FIN AF: 0.0230

Gnomad4 NFE AF: 0.0153

Gnomad4 OTH AF: 0.0568

Alfa AF: 0.0326 Hom.: 21

Bravo AF: 0.0534

Asia WGS AF: 0.145 AC: 502 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.6
DANN	Benign	0.26

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: rs8093048; hg19: chr18-61576608;