rs1052886

Variant names:

• chr6-2889956-A-G
• rs1052886
• NM_004155.6:c.*207T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004155.6(SERPINB9):​c.*207T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 468,126 control chromosomes in the GnomAD database, including 10,439 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 0.18 (2969 hom., cov: 31)
  • Exomes 𝑓: 0.21 (7470 hom.)
• Consequence: SERPINB9 NM_004155.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.736
• Publications: 16 publications found

Genes affected

SERPINB9 (HGNC:8955): (serpin family B member 9) This gene encodes a member of the serine protease inhibitor family which are also known as serpins. The encoded protein belongs to a subfamily of intracellular serpins. This protein inhibits the activity of the effector molecule granzyme B. Overexpression of this protein may prevent cytotoxic T-lymphocytes from eliminating certain tumor cells. A pseudogene of this gene is found on chromosome 6. [provided by RefSeq, Mar 2012]

SERPINB9-AS1 (HGNC:56120): (SERPINB9 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004155.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SERPINB9	NM_004155.6	MANE Select	c.*207T>C		3_prime_UTR	Exon 7 of 7	NP_004146.1	A0A024QZT4
	SERPINB9-AS1	NR_110841.1		n.224+5116A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SERPINB9	ENST00000380698.5	TSL:1 MANE Select	c.*207T>C		3_prime_UTR	Exon 7 of 7	ENSP00000370074.4	P50453
	SERPINB9	ENST00000718363.1		c.*207T>C		3_prime_UTR	Exon 7 of 7	ENSP00000520789.1	P50453
	SERPINB9	ENST00000893932.1		c.*207T>C		3_prime_UTR	Exon 8 of 8	ENSP00000563991.1

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27658 AN: 151940 Hom.: 2967 Cov.: 31

Gnomad AFR AF: 0.0943

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.174

GnomAD4 exome AF: 0.206 AC: 65063 AN: 316068 Hom.: 7470 Cov.: 4 AF XY: 0.205 AC XY: 33199 AN XY: 162160

African (AFR) AF: 0.0960 AC: 1056 AN: 11004

American (AMR) AF: 0.113 AC: 1487 AN: 13122

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 1477 AN: 10618

East Asian (EAS) AF: 0.146 AC: 3947 AN: 26998

South Asian (SAS) AF: 0.107 AC: 1582 AN: 14830

European-Finnish (FIN) AF: 0.348 AC: 7298 AN: 20964

Middle Eastern (MID) AF: 0.115 AC: 176 AN: 1532

European-Non Finnish (NFE) AF: 0.224 AC: 44248 AN: 197246

Other (OTH) AF: 0.192 AC: 3792 AN: 19754

GnomAD4 genome AF: 0.182 AC: 27662 AN: 152058 Hom.: 2969 Cov.: 31 AF XY: 0.184 AC XY: 13646 AN XY: 74316

African (AFR) AF: 0.0940 AC: 3902 AN: 41504

American (AMR) AF: 0.137 AC: 2088 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 529 AN: 3462

East Asian (EAS) AF: 0.129 AC: 665 AN: 5160

South Asian (SAS) AF: 0.115 AC: 554 AN: 4822

European-Finnish (FIN) AF: 0.357 AC: 3764 AN: 10534

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.228 AC: 15514 AN: 67978

Other (OTH) AF: 0.176 AC: 370 AN: 2108

Alfa AF: 0.207 Hom.: 7713

Bravo AF: 0.162

Asia WGS AF: 0.149 AC: 517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.0
DANN	Benign	0.70
PhyloP100		-0.74
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
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: rs1052886; hg19: chr6-2890190;