rs1700488

Positions:

• chr5-135039187-G-A
• chr5-135039187-G-T

Variant summary

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

The NR_105050.1(EPIST):​n.482C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,260 control chromosomes in the GnomAD database, including 4,598 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 0.20 (4598 hom., cov: 33)
  • Exomes 𝑓: 0.061 (0 hom.)
• Consequence: EPIST NR_105050.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283

Genes affected

EPIST (HGNC:49679): (esophagus epithelial intergenic associated transcript)

PITX1-AS1 (HGNC:48332): (PITX1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EPIST	NR_105050.1	n.482C>T		non_coding_transcript_exon_variant	2/2
PITX1-AS1	NR_161235.1	n.267+5647G>A		intron_variant, non_coding_transcript_variant
EPIST	NR_105049.1	n.487C>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EPIST	ENST00000507035.2	n.487C>T		non_coding_transcript_exon_variant	2/2	2
PITX1-AS1	ENST00000624272.3	n.261+5647G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30210 AN: 152076 Hom.: 4562 Cov.: 33

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.0671

Gnomad EAS AF: 0.00174

Gnomad SAS AF: 0.0497

Gnomad FIN AF: 0.0756

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.191

GnomAD4 exome AF: 0.0606 AC: 4 AN: 66 Hom.: 0 Cov.: 0 AF XY: 0.0577 AC XY: 3 AN XY: 52

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.0517

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.199 AC: 30319 AN: 152194 Hom.: 4598 Cov.: 33 AF XY: 0.192 AC XY: 14280 AN XY: 74410

Gnomad4 AFR AF: 0.423

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.0671

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0510

Gnomad4 FIN AF: 0.0756

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.189

Alfa AF: 0.121 Hom.: 517

Bravo AF: 0.221

Asia WGS AF: 0.0520 AC: 182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	3.9
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1700488; hg19: chr5-134374877;