rs7041637

Variant names:

• chr9-21961867-C-A
• rs7041637
• ENST00000404796.3:n.461-67566C>A

Variant summary

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

The ENST00000731046.1(CDKN2A-AS1):​n.647+1348C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 152,082 control chromosomes in the GnomAD database, including 5,401 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 0.25 (5401 hom., cov: 32)
• Consequence: CDKN2A-AS1 ENST00000731046.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583
• Publications: 21 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000731046.1. 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
	ENSG00000264545	ENST00000404796.3	TSL:5	n.461-67566C>A		intron	N/A
	CDKN2A-AS1	ENST00000731046.1		n.647+1348C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37737 AN: 151962 Hom.: 5410 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.248 AC: 37731 AN: 152082 Hom.: 5401 Cov.: 32 AF XY: 0.253 AC XY: 18777 AN XY: 74324

African (AFR) AF: 0.104 AC: 4299 AN: 41502

American (AMR) AF: 0.274 AC: 4186 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1286 AN: 3470

East Asian (EAS) AF: 0.473 AC: 2443 AN: 5162

South Asian (SAS) AF: 0.412 AC: 1987 AN: 4818

European-Finnish (FIN) AF: 0.294 AC: 3100 AN: 10562

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.286 AC: 19427 AN: 67966

Other (OTH) AF: 0.266 AC: 561 AN: 2106

Alfa AF: 0.278 Hom.: 10764

Bravo AF: 0.235

Asia WGS AF: 0.380 AC: 1322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.43
DANN	Benign	0.42
PhyloP100		-0.58

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

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

Other links and lift over

dbSNP: rs7041637;

hg19: chr9-21961866;