rs8085490

Positions:

• chr18-63919151-T-C
• chr18-63919151-T-G

Variant summary

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

The NM_005024.3(SERPINB10):​c.373-637T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 151,374 control chromosomes in the GnomAD database, including 13,942 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 0.37 (13942 hom., cov: 31)
• Consequence: SERPINB10 NM_005024.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SERPINB10	NM_005024.3	c.373-637T>C		intron_variant		ENST00000238508.8
SERPINB10	XM_011526028.1	c.-89T>C		5_prime_UTR_variant	2/6
SERPINB10	XM_011526027.2	c.373-637T>C		intron_variant
SERPINB10	XM_017025793.2	c.373-637T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SERPINB10	ENST00000238508.8	c.373-637T>C		intron_variant		1	NM_005024.3	P1

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56159 AN: 151256 Hom.: 13899 Cov.: 31

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.372 AC: 56261 AN: 151374 Hom.: 13942 Cov.: 31 AF XY: 0.372 AC XY: 27528 AN XY: 73940

Gnomad4 AFR AF: 0.697

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.439

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.369

Alfa AF: 0.208 Hom.: 1857

Bravo AF: 0.402

Asia WGS AF: 0.400 AC: 1388 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	0.83
DANN	Benign	0.53

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: rs8085490; hg19: chr18-61586385;