NM_005024.3:c.123A>T

Variant names:

• chr18-63915633-A-T
• rs8097425
• NM_005024.3:c.123A>T

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP7

The NM_005024.3(SERPINB10):​c.123A>T​(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
• Publications: 33 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]

ENSG00000289724 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (REVEL=0.151).
• BP7: Synonymous conserved (PhyloP=3.17 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005024.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SERPINB10	NM_005024.3	MANE Select	c.123A>T	p.Ile41Ile	synonymous	Exon 2 of 8	NP_005015.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SERPINB10	ENST00000238508.8	TSL:1 MANE Select	c.123A>T	p.Ile41Ile	synonymous	Exon 2 of 8	ENSP00000238508.3
	ENSG00000289724	ENST00000418725.1	TSL:5	c.678A>T	p.Ile226Ile	synonymous	Exon 6 of 7	ENSP00000392381.1
	ENSG00000289724	ENST00000397996.6	TSL:5	c.759A>T	p.Ile253Ile	synonymous	Exon 7 of 8	ENSP00000381082.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	7.4
DANN	Benign	0.69
PhyloP100		3.2
PromoterAI		0.021	Neutral

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: rs8097425; hg19: chr18-61582867;