rs8097425

Positions:

• chr18-63915633-A-C
• chr18-63915633-A-G
• chr18-63915633-A-T

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_005024.3(SERPINB10):​c.123A>C​(p.Ile41Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: SERPINB10 NM_005024.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.17

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 Likely_benign. Variant got -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BP7: Synonymous conserved (PhyloP=3.17 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SERPINB10	NM_005024.3	c.123A>C	p.Ile41Ile	synonymous_variant	2/8	ENST00000238508.8	NP_005015.1
SERPINB10	XM_011526027.2	c.123A>C	p.Ile41Ile	synonymous_variant	3/9		XP_011524329.1
SERPINB10	XM_017025793.2	c.123A>C	p.Ile41Ile	synonymous_variant	2/8		XP_016881282.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SERPINB10	ENST00000238508.8	c.123A>C	p.Ile41Ile	synonymous_variant	2/8	1	NM_005024.3	ENSP00000238508.3
ENSG00000289724	ENST00000397996.6	c.759A>C	p.Ile253Ile	synonymous_variant	7/8	5		ENSP00000381082.2
ENSG00000289724	ENST00000418725.1	c.678A>C	p.Ile226Ile	synonymous_variant	6/7	5		ENSP00000392381.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	7.9
DANN	Benign	0.71

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs8097425; hg19: chr18-61582867;