rs1324208

Variant names:

• chr9-2282951-G-A
• rs1324208

Your query was ambiguous. Multiple possible variants found:

• chr9-2282951-G-A
• chr9-2282951-G-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 0.285 in 152,086 control chromosomes in the GnomAD database, including 7,309 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 0.28 (7309 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.411
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.693 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: 0.285 AC: 43268 AN: 151968 Hom.: 7302 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.285 AC: 43304 AN: 152086 Hom.: 7309 Cov.: 32 AF XY: 0.295 AC XY: 21905 AN XY: 74330

African (AFR) AF: 0.151 AC: 6252 AN: 41512

American (AMR) AF: 0.347 AC: 5305 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1138 AN: 3472

East Asian (EAS) AF: 0.712 AC: 3664 AN: 5146

South Asian (SAS) AF: 0.500 AC: 2409 AN: 4818

European-Finnish (FIN) AF: 0.340 AC: 3588 AN: 10566

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19912 AN: 67974

Other (OTH) AF: 0.295 AC: 623 AN: 2110

Alfa AF: 0.290 Hom.: 29851

Bravo AF: 0.279

Asia WGS AF: 0.549 AC: 1907 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.9
DANN	Benign	0.62
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs1324208; hg19: chr9-2282951;