chr4-25162050-A-G

Position:

• chr4-25162050-A-G

Variant summary

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

The NR_037934.1(SEPSECS-AS1):​n.82+1297A>G 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 0.503 in 152,082 control chromosomes in the GnomAD database, including 20,047 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 0.50 (20047 hom., cov: 33)
• Consequence: SEPSECS-AS1 NR_037934.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0600

Genes affected

SEPSECS-AS1 (HGNC:27737): (SEPSECS antisense RNA 1 (head to head))

PI4K2B (HGNC:18215): (phosphatidylinositol 4-kinase type 2 beta) This gene encodes a member of the type II PI4 kinase protein family. The encoded protein is primarily cytosolic and contributes to overall PI4-kinase activity along with other protein family members. This protein is involved in early T cell activation. [provided by RefSeq, Dec 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SEPSECS-AS1	NR_037934.1	n.82+1297A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SEPSECS-AS1	ENST00000507794.2	n.82+1297A>G		intron_variant, non_coding_transcript_variant		2
PI4K2B	ENST00000512921.4	c.-21+1297A>G		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76457 AN: 151964 Hom.: 20055 Cov.: 33

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.503 AC: 76480 AN: 152082 Hom.: 20047 Cov.: 33 AF XY: 0.503 AC XY: 37404 AN XY: 74370

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.485

Gnomad4 ASJ AF: 0.430

Gnomad4 EAS AF: 0.288

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.688

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.504

Alfa AF: 0.543 Hom.: 44891

Bravo AF: 0.486

Asia WGS AF: 0.378 AC: 1314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.4
DANN	Benign	0.88

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs11937742; hg19: chr4-25163672;