rs2232707

Variant names:

• chr14-94288468-G-A
• rs2232707
• NM_001100607.3:c.810C>T

Your query was ambiguous. Multiple possible variants found:

• chr14-94288468-G-A
• chr14-94288468-G-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_Strong BP7 BS2

The NM_001100607.3(SERPINA10):​c.810C>T​(p.Tyr270Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00105 in 1,614,136 control chromosomes in the GnomAD database, including 4 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 0.0017 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00098 (4 hom.)
• Consequence: SERPINA10 NM_001100607.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.88

Genes affected

SERPINA10 (HGNC:15996): (serpin family A member 10) The protein encoded by this gene belongs to the serpin family. It is predominantly expressed in the liver and secreted in plasma. It inhibits the activity of coagulation factors Xa and XIa in the presence of protein Z, calcium and phospholipid. Mutations in this gene are associated with venous thrombosis. Alternatively spliced transcript variants have been found for this gene.[provided by RefSeq, May 2010]

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP7: Synonymous conserved (PhyloP=1.88 with no splicing effect.
• BS2: High Homozygotes in GnomAdExome4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SERPINA10	NM_001100607.3	c.810C>T	p.Tyr270Tyr	synonymous_variant	Exon 3 of 5	ENST00000261994.9	NP_001094077.1
SERPINA10	NM_016186.3	c.810C>T	p.Tyr270Tyr	synonymous_variant	Exon 3 of 5		NP_057270.1
SERPINA10	XM_017021353.2	c.930C>T	p.Tyr310Tyr	synonymous_variant	Exon 4 of 6		XP_016876842.1
SERPINA10	XM_005267733.6	c.810C>T	p.Tyr270Tyr	synonymous_variant	Exon 3 of 5		XP_005267790.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SERPINA10	ENST00000261994.9	c.810C>T	p.Tyr270Tyr	synonymous_variant	Exon 3 of 5	1	NM_001100607.3	ENSP00000261994.4
SERPINA10	ENST00000554723.5	c.930C>T	p.Tyr310Tyr	synonymous_variant	Exon 3 of 5	1		ENSP00000450896.1
SERPINA10	ENST00000393096.5	c.810C>T	p.Tyr270Tyr	synonymous_variant	Exon 3 of 5	1		ENSP00000376809.1
SERPINA10	ENST00000554173.1	c.810C>T	p.Tyr270Tyr	synonymous_variant	Exon 2 of 4	1		ENSP00000450971.1

Frequencies

GnomAD3 genomes AF: 0.00166 AC: 253 AN: 152128 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000555

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000589

Gnomad ASJ AF: 0.000865

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00763

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00197

Gnomad OTH AF: 0.00143

GnomAD3 exomes AF: 0.00155 AC: 390 AN: 251472 Hom.: 2 AF XY: 0.00152 AC XY: 206 AN XY: 135904

Gnomad AFR exome AF: 0.000615

Gnomad AMR exome AF: 0.0000289

Gnomad ASJ exome AF: 0.000397

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000653

Gnomad FIN exome AF: 0.00841

Gnomad NFE exome AF: 0.00161

Gnomad OTH exome AF: 0.00130

GnomAD4 exome AF: 0.000981 AC: 1434 AN: 1461890 Hom.: 4 Cov.: 32 AF XY: 0.00104 AC XY: 759 AN XY: 727246

Gnomad4 AFR exome AF: 0.000478

Gnomad4 AMR exome AF: 0.0000671

Gnomad4 ASJ exome AF: 0.000421

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.0000464

Gnomad4 FIN exome AF: 0.00719

Gnomad4 NFE exome AF: 0.000868

Gnomad4 OTH exome AF: 0.000795

GnomAD4 genome AF: 0.00166 AC: 253 AN: 152246 Hom.: 0 Cov.: 32 AF XY: 0.00192 AC XY: 143 AN XY: 74430

Gnomad4 AFR AF: 0.000554

Gnomad4 AMR AF: 0.000588

Gnomad4 ASJ AF: 0.000865

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00763

Gnomad4 NFE AF: 0.00197

Gnomad4 OTH AF: 0.00142

Alfa AF: 0.00194 Hom.: 2

Bravo AF: 0.000899

EpiCase AF: 0.00109

EpiControl AF: 0.000593

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.9
DANN	Benign	0.26

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

Publications

LitVar

Other links and lift over

dbSNP: rs2232707; hg19: chr14-94754805;