19-7634319-C-T

Variant summary

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

The ENST00000601797.1(ENSG00000268204):n.720-430G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,114 control chromosomes in the GnomAD database, including 7,137 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 (7137 hom., cov: 32)
• Consequence: ENST00000601797.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.588

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STXBP2	NM_001414484.1	c.-60+3473C>T		intron_variant
PCP2	XM_006722639.4	c.-60-1489G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000601797.1	n.720-430G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44299 AN: 151994 Hom.: 7129 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.291 AC: 44320 AN: 152114 Hom.: 7137 Cov.: 32 AF XY: 0.292 AC XY: 21688 AN XY: 74372

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.246

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.286

Gnomad4 FIN AF: 0.418

Gnomad4 NFE AF: 0.369

Gnomad4 OTH AF: 0.305

Alfa AF: 0.324 Hom.: 3923

Bravo AF: 0.272

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.2
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3745364; hg19: chr19-7699205;