10-110871453-G-A

Variant names:

• chr10-110871453-G-A
• rs6585018
• ENST00000416249.1:n.260G>A

Variant summary

Our verdict is Benign. The variant received -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: ENSG00000232470 ENST00000416249.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.613
• Publications: 6 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=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000416249.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000232470	ENST00000416249.1	TSL:2	n.260G>A		non_coding_transcript_exon	Exon 2 of 2
	PDCD4-AS1	ENST00000813598.1		n.414C>T		non_coding_transcript_exon	Exon 2 of 2
	PDCD4-AS1	ENST00000813599.1		n.190C>T		non_coding_transcript_exon	Exon 2 of 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

African (AFR) AF: 1.00 AC: 6 AN: 6

American (AMR) AF: 1.00 AC: 2 AN: 2

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.917 AC: 11 AN: 12

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.961 AC: 123 AN: 128

Other (OTH) AF: 1.00 AC: 12 AN: 12

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

African (AFR) AF: 0.822 AC: 34128 AN: 41520

American (AMR) AF: 0.958 AC: 14655 AN: 15300

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

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

South Asian (SAS) AF: 0.897 AC: 4320 AN: 4818

European-Finnish (FIN) AF: 0.945 AC: 10039 AN: 10622

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.955 AC: 64989 AN: 68032

Other (OTH) AF: 0.930 AC: 1964 AN: 2112

Alfa AF: 0.906 Hom.: 20108

Bravo AF: 0.916

Asia WGS AF: 0.945 AC: 3284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.72
DANN	Benign	0.75
PhyloP100		-0.61
PromoterAI		0.011	Neutral

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6585018;

hg19: chr10-112631211;