6-2864061-T-C

Variant names:

• chr6-2864061-T-C
• rs380779
• ENST00000420981.4:n.231-6066A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000420981.4(SERPINB9P1):​n.231-6066A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 151,834 control chromosomes in the GnomAD database, including 6,745 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 0.28 (6745 hom., cov: 32)
• Consequence: SERPINB9P1 ENST00000420981.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.752

Genes affected

SERPINB9P1 (HGNC:28590): (serpin family B member 9 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SERPINB9P1	NR_033851.1	n.219-8371A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SERPINB9P1	ENST00000420981.4	n.231-6066A>G		intron_variant	Intron 2 of 3	1
SERPINB9P1	ENST00000545177.5	n.136-6070A>G		intron_variant	Intron 2 of 3	3
SERPINB9P1	ENST00000654948.2	n.322-6066A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43203 AN: 151716 Hom.: 6749 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.310

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.285 AC: 43206 AN: 151834 Hom.: 6745 Cov.: 32 AF XY: 0.288 AC XY: 21364 AN XY: 74188

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.459

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.308

Alfa AF: 0.322 Hom.: 11057

Bravo AF: 0.292

Asia WGS AF: 0.387 AC: 1347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.34

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs380779; hg19: chr6-2864295;