10-110871099-C-A

Variant names:

• chr10-110871099-C-A
• rs1322997
• ENST00000416249.1:n.100-194C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000416249.1(ENSG00000232470):​n.100-194C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.925 in 152,246 control chromosomes in the GnomAD database, including 65,276 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 (65276 hom., cov: 31)
• Consequence: ENSG00000232470 ENST00000416249.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307
• Publications: 4 publications found

Genes affected

ENSG00000232470 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• 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 rank	MANE	Protein	UniProt
PDCD4-AS1	NR_026932.1	n.-195G>T		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000232470	ENST00000416249.1	n.100-194C>A		intron_variant	Intron 1 of 1	2
PDCD4-AS1	ENST00000420367.3	n.341-661G>T		intron_variant	Intron 1 of 1	2
PDCD4-AS1	ENST00000813596.1	n.56+589G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.925 AC: 140655 AN: 152128 Hom.: 65224 Cov.: 31

Gnomad AFR AF: 0.849

Gnomad AMI AF: 0.985

Gnomad AMR AF: 0.960

Gnomad ASJ AF: 0.918

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.895

Gnomad FIN AF: 0.945

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.955

Gnomad OTH AF: 0.936

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

GnomAD4 genome AF: 0.925 AC: 140766 AN: 152246 Hom.: 65276 Cov.: 31 AF XY: 0.925 AC XY: 68872 AN XY: 74450

African (AFR) AF: 0.849 AC: 35251 AN: 41522

American (AMR) AF: 0.960 AC: 14692 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.918 AC: 3186 AN: 3472

East Asian (EAS) AF: 0.996 AC: 5167 AN: 5186

South Asian (SAS) AF: 0.896 AC: 4317 AN: 4818

European-Finnish (FIN) AF: 0.945 AC: 10016 AN: 10598

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.955 AC: 64990 AN: 68030

Other (OTH) AF: 0.937 AC: 1978 AN: 2112

Alfa AF: 0.939 Hom.: 26479

Bravo AF: 0.925

Asia WGS AF: 0.947 AC: 3291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.56
DANN	Benign	0.52
PhyloP100		-0.31
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Other links and lift over

dbSNP: rs1322997; hg19: chr10-112630857;