ENST00000626206.1:n.222+2498C>T

Variant names:

• chr2-54677326-G-A
• rs2971884
• ENST00000626206.1:n.222+2498C>T

Variant summary

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

The ENST00000626206.1(SPTBN1-AS2):​n.222+2498C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.068 in 152,310 control chromosomes in the GnomAD database, including 383 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 0.068 (383 hom., cov: 32)
• Consequence: SPTBN1-AS2 ENST00000626206.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.308
• Publications: 3 publications found

Genes affected

SPTBN1-AS2 (HGNC:40563): (SPTBN1 antisense RNA 2)

ENSG00000299013 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0852 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPTBN1-AS2	NR_186176.1	n.222+2498C>T		intron_variant	Intron 1 of 2
LOC105374653	XR_940104.2	n.254+2691G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPTBN1-AS2	ENST00000626206.1	n.222+2498C>T		intron_variant	Intron 1 of 3	5
ENSG00000299013	ENST00000759811.1	n.747+2691G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0680 AC: 10355 AN: 152192 Hom.: 383 Cov.: 32

Gnomad AFR AF: 0.0875

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0654

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0290

Gnomad FIN AF: 0.0564

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0648

Gnomad OTH AF: 0.0688

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

GnomAD4 genome AF: 0.0680 AC: 10364 AN: 152310 Hom.: 383 Cov.: 32 AF XY: 0.0676 AC XY: 5034 AN XY: 74480

African (AFR) AF: 0.0876 AC: 3640 AN: 41564

American (AMR) AF: 0.0654 AC: 1000 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 354 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5192

South Asian (SAS) AF: 0.0288 AC: 139 AN: 4828

European-Finnish (FIN) AF: 0.0564 AC: 599 AN: 10614

Middle Eastern (MID) AF: 0.110 AC: 32 AN: 292

European-Non Finnish (NFE) AF: 0.0648 AC: 4405 AN: 68024

Other (OTH) AF: 0.0681 AC: 144 AN: 2114

Alfa AF: 0.0685 Hom.: 509

Bravo AF: 0.0703

Asia WGS AF: 0.0180 AC: 63 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.2
DANN	Benign	0.66
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs2971884; hg19: chr2-54904463;