6-159085568-C-T

Position:

• chr6-159085568-C-T

Variant summary

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

The XM_047419645.1(LOC112267968):​c.323+10161G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.751 in 151,840 control chromosomes in the GnomAD database, including 43,890 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 0.75 (43890 hom., cov: 29)
• Consequence: LOC112267968 XM_047419645.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.810

Genes affected

LOC112267968 (HGNC:):

TAGAP-AS1 (HGNC:55239): (TAGAP antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -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 = 0.911 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC112267968	XM_047419645.1	c.323+10161G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000642829.1	n.500+10161G>A		intron_variant, non_coding_transcript_variant
TAGAP-AS1	ENST00000643132.2	n.829-985C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.751 AC: 113972 AN: 151722 Hom.: 43828 Cov.: 29

Gnomad AFR AF: 0.894

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.794

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.933

Gnomad SAS AF: 0.784

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.738

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

GnomAD4 genome AF: 0.751 AC: 114095 AN: 151840 Hom.: 43890 Cov.: 29 AF XY: 0.758 AC XY: 56251 AN XY: 74166

Gnomad4 AFR AF: 0.894

Gnomad4 AMR AF: 0.794

Gnomad4 ASJ AF: 0.662

Gnomad4 EAS AF: 0.933

Gnomad4 SAS AF: 0.783

Gnomad4 FIN AF: 0.733

Gnomad4 NFE AF: 0.649

Gnomad4 OTH AF: 0.741

Alfa AF: 0.677 Hom.: 33750

Bravo AF: 0.763

Asia WGS AF: 0.880 AC: 3061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.3
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2451258; hg19: chr6-159506600;