rs2472496

Variant names:

• chr9-104933072-G-A
• rs2472496
• ENST00000820514.1:n.1164+5162G>A

Variant summary

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

The ENST00000820514.1(ENSG00000226334):​n.1164+5162G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 151,986 control chromosomes in the GnomAD database, including 28,477 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 0.61 (28477 hom., cov: 31)
• Consequence: ENSG00000226334 ENST00000820514.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 15 publications found

Genes affected

ENSG00000226334 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376196	NR_188620.1	n.1339+3348G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226334	ENST00000820514.1	n.1164+5162G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92601 AN: 151868 Hom.: 28460 Cov.: 31

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.691

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.610 AC: 92662 AN: 151986 Hom.: 28477 Cov.: 31 AF XY: 0.613 AC XY: 45521 AN XY: 74274

African (AFR) AF: 0.646 AC: 26789 AN: 41438

American (AMR) AF: 0.649 AC: 9912 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.701 AC: 2429 AN: 3466

East Asian (EAS) AF: 0.450 AC: 2321 AN: 5160

South Asian (SAS) AF: 0.673 AC: 3247 AN: 4822

European-Finnish (FIN) AF: 0.629 AC: 6633 AN: 10550

Middle Eastern (MID) AF: 0.699 AC: 204 AN: 292

European-Non Finnish (NFE) AF: 0.577 AC: 39229 AN: 67974

Other (OTH) AF: 0.597 AC: 1259 AN: 2110

Alfa AF: 0.594 Hom.: 10392

Bravo AF: 0.611

Asia WGS AF: 0.550 AC: 1911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.1
DANN	Benign	0.50
PhyloP100		0.064

Splicing

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

Other links and lift over

dbSNP: rs2472496; hg19: chr9-107695353;