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 ENST00000404796.3(ENSG00000264545):​n.461-67566C>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: ENSG00000264545 ENST00000404796.3 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.

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.461-67566C>A		intron_variant	Intron 4 of 4	5
CDKN2A-AS1	ENST00000731046.1	n.647+1348C>A		intron_variant	Intron 1 of 1

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 v4.3

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

Other links and lift over

dbSNP: rs7041637; hg19: chr9-21961866;