rs6585018

chr10-110871453-G-Achr10-110871453-G-Cchr10-110871453-G-T

Variant summary

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

The ENST00000416249.1(ENSG00000232470):n.260G>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 0.917 in 152,432 control chromosomes in the GnomAD database, including 64,344 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 0.92 (64267 hom., cov: 32)
  • Exomes 𝑓: 0.96 (77 hom.)
• Consequence: ENST00000416249.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.613

Genes affected

(HGNC:):

PDCD4-AS1 (HGNC:27425): (PDCD4 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000416249.1	n.260G>A		non_coding_transcript_exon_variant	2/2	2
PDCD4-AS1	ENST00000420367.2	n.227+574C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.917 AC: 139522 AN: 152150 Hom.: 64227 Cov.: 32

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.985

Gnomad AMR AF: 0.958

Gnomad ASJ AF: 0.918

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.896

Gnomad FIN AF: 0.945

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.955

Gnomad OTH AF: 0.929

GnomAD4 exome AF: 0.963 AC: 158 AN: 164 Hom.: 77 Cov.: 0 AF XY: 0.984 AC XY: 122 AN XY: 124

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 1.00

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.917

Gnomad4 NFE exome AF: 0.961

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.917 AC: 139617 AN: 152268 Hom.: 64267 Cov.: 32 AF XY: 0.918 AC XY: 68316 AN XY: 74450

Gnomad4 AFR AF: 0.822

Gnomad4 AMR AF: 0.958

Gnomad4 ASJ AF: 0.918

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.897

Gnomad4 FIN AF: 0.945

Gnomad4 NFE AF: 0.955

Gnomad4 OTH AF: 0.930

Alfa AF: 0.938 Hom.: 14690

Bravo AF: 0.916

Asia WGS AF: 0.945 AC: 3284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	0.72
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6585018; hg19: chr10-112631211;