rs9332420

Variant names:

• chr2-35354625-A-G
• rs9332420

Your query was ambiguous. Multiple possible variants found:

• chr2-35354625-A-G
• chr2-35354625-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 0.649 in 152,110 control chromosomes in the GnomAD database, including 33,182 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 0.65 (33182 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340
• Publications: 5 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 (NFE) allele frequency at 95% confidence interval = 0.701 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: 0.649 AC: 98718 AN: 151992 Hom.: 33173 Cov.: 33

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.783

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.665

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

GnomAD4 genome AF: 0.649 AC: 98764 AN: 152110 Hom.: 33182 Cov.: 33 AF XY: 0.636 AC XY: 47319 AN XY: 74346

African (AFR) AF: 0.684 AC: 28367 AN: 41488

American (AMR) AF: 0.518 AC: 7909 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.762 AC: 2645 AN: 3472

East Asian (EAS) AF: 0.207 AC: 1072 AN: 5170

South Asian (SAS) AF: 0.429 AC: 2068 AN: 4820

European-Finnish (FIN) AF: 0.603 AC: 6388 AN: 10586

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.706 AC: 47993 AN: 67990

Other (OTH) AF: 0.660 AC: 1388 AN: 2102

Alfa AF: 0.671 Hom.: 26444

Bravo AF: 0.646

Asia WGS AF: 0.363 AC: 1268 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	4.6
DANN	Benign	0.70
PhyloP100		-0.034

Splicing

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

Other links and lift over

dbSNP: rs9332420; hg19: chr2-35579691;