rs6779973

Positions:

• chr3-170812792-A-G
• chr3-170812792-A-T

Variant summary

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

The ENST00000644993.1(SLC7A14-AS1):​n.294-47191A>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 0.33 in 152,096 control chromosomes in the GnomAD database, including 10,703 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 0.33 (10703 hom., cov: 32)
• Consequence: SLC7A14-AS1 ENST00000644993.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.326

Genes affected

SLC7A14-AS1 (HGNC:54092): (SLC7A14 antisense RNA 1)

LOC105374211 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374211	XR_924701.2	n.1211-24521A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC7A14-AS1	ENST00000644993.1	n.294-47191A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50102 AN: 151978 Hom.: 10674 Cov.: 32

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.330 AC: 50193 AN: 152096 Hom.: 10703 Cov.: 32 AF XY: 0.334 AC XY: 24869 AN XY: 74358

Gnomad4 AFR AF: 0.574

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.669

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.230

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.317

Alfa AF: 0.216 Hom.: 6054

Bravo AF: 0.349

Asia WGS AF: 0.505 AC: 1755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.61
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6779973; hg19: chr3-170530581;