6-2864061-T-C

Variant names:

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

Variant summary

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

The ENST00000786925.1(SERPINB9P1):​n.572A>G variant causes a non coding transcript exon 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 ENST00000786925.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.752
• Publications: 15 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000786925.1. 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
	SERPINB9P1	NR_033851.1		n.219-8371A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SERPINB9P1	ENST00000420981.4	TSL:1	n.231-6066A>G		intron	N/A
	SERPINB9P1	ENST00000786925.1		n.572A>G		non_coding_transcript_exon	Exon 2 of 4
	SERPINB9P1	ENST00000545177.5	TSL:3	n.136-6070A>G		intron	N/A

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

African (AFR) AF: 0.173 AC: 7171 AN: 41368

American (AMR) AF: 0.373 AC: 5700 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1121 AN: 3462

East Asian (EAS) AF: 0.459 AC: 2372 AN: 5164

South Asian (SAS) AF: 0.448 AC: 2154 AN: 4810

European-Finnish (FIN) AF: 0.205 AC: 2158 AN: 10540

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21362 AN: 67916

Other (OTH) AF: 0.308 AC: 650 AN: 2110

Alfa AF: 0.319 Hom.: 13407

Bravo AF: 0.292

Asia WGS AF: 0.387 AC: 1347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.34
PhyloP100		-0.75

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs380779;

hg19: chr6-2864295;