rs315791

Positions:

• chr5-170308916-A-C
• chr5-170308916-A-T

Variant summary

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

The ENST00000511921.2(ENSG00000250274):​n.2057T>G 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 0.471 in 152,036 control chromosomes in the GnomAD database, including 16,998 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 0.47 (16998 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000250274 ENST00000511921.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.253

Genes affected

ENSG00000250274 (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 = 0.509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100128059	NR_147701.1	n.1967T>G		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000250274	ENST00000511921.2	n.2057T>G		non_coding_transcript_exon_variant	2/2	2
LINC01366	ENST00000653905.1	n.84+1111A>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71554 AN: 151918 Hom.: 16981 Cov.: 32

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.489

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.471 AC: 71601 AN: 152036 Hom.: 16998 Cov.: 32 AF XY: 0.469 AC XY: 34831 AN XY: 74302

Gnomad4 AFR AF: 0.419

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.505

Gnomad4 EAS AF: 0.525

Gnomad4 SAS AF: 0.402

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.497

Alfa AF: 0.496 Hom.: 38082

Bravo AF: 0.478

Asia WGS AF: 0.470 AC: 1633 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	2.8
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs315791; hg19: chr5-169735920;