rs8085490

Variant names:

• chr18-63919151-T-C
• rs8085490
• NM_005024.3:c.373-637T>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

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

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 = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SERPINB10	NM_005024.3	c.373-637T>C		intron_variant	Intron 4 of 7	ENST00000238508.8	NP_005015.1
SERPINB10	XM_011526028.1	c.-89T>C		5_prime_UTR_variant	Exon 2 of 6		XP_011524330.1
SERPINB10	XM_011526027.2	c.373-637T>C		intron_variant	Intron 5 of 8		XP_011524329.1
SERPINB10	XM_017025793.2	c.373-637T>C		intron_variant	Intron 4 of 7		XP_016881282.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SERPINB10	ENST00000238508.8	c.373-637T>C		intron_variant	Intron 4 of 7	1	NM_005024.3	ENSP00000238508.3

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

African (AFR) AF: 0.697 AC: 28731 AN: 41240

American (AMR) AF: 0.399 AC: 6053 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 565 AN: 3464

East Asian (EAS) AF: 0.439 AC: 2247 AN: 5118

South Asian (SAS) AF: 0.285 AC: 1368 AN: 4808

European-Finnish (FIN) AF: 0.226 AC: 2362 AN: 10468

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.206 AC: 13955 AN: 67806

Other (OTH) AF: 0.369 AC: 774 AN: 2098

Alfa AF: 0.214 Hom.: 2277

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
PhyloP100		-1.5
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: rs8085490; hg19: chr18-61586385;