3-170737156-T-C

Position:

• chr3-170737156-T-C

Variant summary

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

The NR_135556.1(SLC7A14-AS1):​n.766+7461T>C 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 0.278 in 151,554 control chromosomes in the GnomAD database, including 6,364 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 0.28 (6364 hom., cov: 30)
• Consequence: SLC7A14-AS1 NR_135556.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC7A14-AS1	NR_135556.1	n.766+7461T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC7A14-AS1	ENST00000480067.1	n.769+7461T>C		intron_variant, non_coding_transcript_variant		1
SLC7A14-AS1	ENST00000644993.1	n.293+28962T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42128 AN: 151440 Hom.: 6359 Cov.: 30

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.278 AC: 42150 AN: 151554 Hom.: 6364 Cov.: 30 AF XY: 0.285 AC XY: 21104 AN XY: 74016

Gnomad4 AFR AF: 0.320

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.595

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.305

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.270

Alfa AF: 0.110 Hom.: 181

Bravo AF: 0.283

Asia WGS AF: 0.480 AC: 1668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.19
DANN	Benign	0.061

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs577098; hg19: chr3-170454945; COSMIC: COSV72116348; COSMIC: COSV72116348;