18-63908338-T-A

Variant names:

• chr18-63908338-T-A
• rs1006960
• NM_005024.3:c.-10+298T>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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: Benign. The variant received -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.

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.-10+298T>A		intron	N/A	NP_005015.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SERPINB10	ENST00000238508.8	TSL:1 MANE Select	c.-10+298T>A		intron	N/A	ENSP00000238508.3
	ENSG00000289724	ENST00000418725.1	TSL:5	c.546+5363T>A		intron	N/A	ENSP00000392381.1
	ENSG00000289724	ENST00000397996.6	TSL:5	c.627+298T>A		intron	N/A	ENSP00000381082.2

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

African (AFR) AF: 0.363 AC: 15045 AN: 41456

American (AMR) AF: 0.370 AC: 5642 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 638 AN: 3468

East Asian (EAS) AF: 0.480 AC: 2462 AN: 5132

South Asian (SAS) AF: 0.294 AC: 1418 AN: 4822

European-Finnish (FIN) AF: 0.233 AC: 2470 AN: 10580

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.220 AC: 14941 AN: 67942

Other (OTH) AF: 0.308 AC: 649 AN: 2108

Alfa AF: 0.140 Hom.: 244

Bravo AF: 0.302

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.6
DANN	Benign	0.78
PhyloP100		0.051
PromoterAI		-0.13	Neutral
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: rs1006960; hg19: chr18-61575572;