6-139324158-T-C

Variant names:

• chr6-139324158-T-C
• rs9484261
• ENST00000650173.1:n.509+37256T>C

Variant summary

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

The ENST00000650173.1(ENSG00000226571):​n.509+37256T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 151,928 control chromosomes in the GnomAD database, including 10,681 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 0.36 (10681 hom., cov: 31)
• Consequence: ENSG00000226571 ENST00000650173.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.101

Genes affected

ENSG00000226571 (HGNC:):

TXLNB (HGNC:21617): (taxilin beta) Predicted to enable syntaxin binding activity. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TXLNB	XM_005266836.2	c.-679A>G		upstream_gene_variant			XP_005266893.1
TXLNB	XM_024446341.2	c.-777A>G		upstream_gene_variant			XP_024302109.1
TXLNB	XM_047418252.1	c.-931A>G		upstream_gene_variant			XP_047274208.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226571	ENST00000650173.1	n.509+37256T>C		intron_variant	Intron 4 of 7

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54000 AN: 151810 Hom.: 10655 Cov.: 31

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.00617

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.356 AC: 54076 AN: 151928 Hom.: 10681 Cov.: 31 AF XY: 0.357 AC XY: 26479 AN XY: 74264

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.00618

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.316

Alfa AF: 0.306 Hom.: 10451

Bravo AF: 0.353

Asia WGS AF: 0.174 AC: 609 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.4
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9484261; hg19: chr6-139645295;