rs269782

Positions:

• chr5-140165717-G-A

Variant summary

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

The ENST00000607850.1(ENSG00000254363):​n.3765G>A 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 0.239 in 151,976 control chromosomes in the GnomAD database, including 4,390 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 0.24 (4388 hom., cov: 30)
  • Exomes 𝑓: 0.27 (2 hom.)
• Consequence: ENSG00000254363 ENST00000607850.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.102

Genes affected

ENSG00000254363 (HGNC:):

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 = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101929719	NR_130738.1	n.203+905G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000254363	ENST00000607850.1	n.3765G>A		non_coding_transcript_exon_variant	1/3	5
ENSG00000254363	ENST00000523154.5	n.203+905G>A		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36286 AN: 151828 Hom.: 4371 Cov.: 30

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.217

GnomAD4 exome AF: 0.267 AC: 8 AN: 30 Hom.: 2 Cov.: 0 AF XY: 0.318 AC XY: 7 AN XY: 22

Gnomad4 AFR exome AF: 0.500

Gnomad4 SAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.273

GnomAD4 genome AF: 0.239 AC: 36346 AN: 151946 Hom.: 4388 Cov.: 30 AF XY: 0.241 AC XY: 17893 AN XY: 74228

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.237

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.277

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.220

Alfa AF: 0.235 Hom.: 699

Bravo AF: 0.238

Asia WGS AF: 0.288 AC: 999 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	8.1
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs269782; hg19: chr5-139545302;