rs2472519

Variant names:

• chr9-104953597-A-G
• rs2472519

Your query was ambiguous. Multiple possible variants found:

• chr9-104953597-A-G
• chr9-104953597-A-T

Variant summary

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

The variant allele was found at a frequency of 0.224 in 152,042 control chromosomes in the GnomAD database, including 3,927 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 0.22 (3927 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.924
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.335 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

Frequencies

GnomAD3 genomes AF: 0.224 AC: 34080 AN: 151924 Hom.: 3930 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.224 AC: 34094 AN: 152042 Hom.: 3927 Cov.: 32 AF XY: 0.227 AC XY: 16856 AN XY: 74272

African (AFR) AF: 0.209 AC: 8681 AN: 41476

American (AMR) AF: 0.208 AC: 3183 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 947 AN: 3466

East Asian (EAS) AF: 0.349 AC: 1800 AN: 5162

South Asian (SAS) AF: 0.303 AC: 1458 AN: 4812

European-Finnish (FIN) AF: 0.270 AC: 2846 AN: 10556

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14448 AN: 67972

Other (OTH) AF: 0.226 AC: 479 AN: 2116

Alfa AF: 0.224 Hom.: 10816

Bravo AF: 0.222

Asia WGS AF: 0.322 AC: 1118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.33
DANN	Benign	0.71
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs2472519; hg19: chr9-107715878;