chr9-21966222-G-A

Variant names:

• chr9-21966222-G-A
• rs3731257
• ENST00000404796.3:n.461-63211G>A

Variant summary

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

The ENST00000404796.3(ENSG00000264545):​n.461-63211G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 152,182 control chromosomes in the GnomAD database, including 4,765 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 0.23 (4765 hom., cov: 32)
• Consequence: ENSG00000264545 ENST00000404796.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.144
• Publications: 36 publications found

Genes affected

ENSG00000264545 (HGNC:):

CDKN2A-AS1 (HGNC:23831): (CDKN2A antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000264545	ENST00000404796.3	n.461-63211G>A		intron_variant	Intron 4 of 4	5
CDKN2A-AS1	ENST00000731046.1	n.648-917G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35107 AN: 152062 Hom.: 4771 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.324

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.231 AC: 35106 AN: 152182 Hom.: 4765 Cov.: 32 AF XY: 0.235 AC XY: 17467 AN XY: 74404

African (AFR) AF: 0.100 AC: 4154 AN: 41558

American (AMR) AF: 0.265 AC: 4045 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1117 AN: 3470

East Asian (EAS) AF: 0.527 AC: 2724 AN: 5172

South Asian (SAS) AF: 0.400 AC: 1929 AN: 4818

European-Finnish (FIN) AF: 0.243 AC: 2578 AN: 10588

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.260 AC: 17653 AN: 67972

Other (OTH) AF: 0.247 AC: 522 AN: 2110

Alfa AF: 0.251 Hom.: 10468

Bravo AF: 0.222

Asia WGS AF: 0.394 AC: 1372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.59
PhyloP100		0.14

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs3731257; hg19: chr9-21966221; COSMIC: COSV58690109;