rs1006960

Positions:

• chr18-63908338-T-A
• chr18-63908338-T-C

Variant summary

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

The NM_005024.3(SERPINB10):​c.-10+298T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 151,954 control chromosomes in the GnomAD database, including 6,821 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 0.29 (6821 hom., cov: 32)
• Consequence: SERPINB10 NM_005024.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0510

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SERPINB10	NM_005024.3	c.-10+298T>A		intron_variant		ENST00000238508.8
SERPINB10	XM_011526027.2	c.-84+298T>A		intron_variant
SERPINB10	XM_017025793.2	c.-10+298T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SERPINB10	ENST00000238508.8	c.-10+298T>A		intron_variant		1	NM_005024.3	P1

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43426 AN: 151836 Hom.: 6800 Cov.: 32

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.286 AC: 43482 AN: 151954 Hom.: 6821 Cov.: 32 AF XY: 0.289 AC XY: 21479 AN XY: 74264

Gnomad4 AFR AF: 0.363

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.220

Gnomad4 OTH AF: 0.308

Alfa AF: 0.140 Hom.: 244

Bravo AF: 0.302

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.6
DANN	Benign	0.78

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: rs1006960; hg19: chr18-61575572;