rs9332446

Variant names:

• chr10-44020973-G-A
• rs9332446

Your query was ambiguous. Multiple possible variants found:

• chr10-44020973-G-A
• chr10-44020973-G-C
• chr10-44020973-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.39 in 152,044 control chromosomes in the GnomAD database, including 13,363 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 0.39 (13363 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.451

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.508 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: 0.390 AC: 59226 AN: 151926 Hom.: 13358 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.390 AC: 59238 AN: 152044 Hom.: 13363 Cov.: 32 AF XY: 0.388 AC XY: 28866 AN XY: 74306

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.360

Gnomad4 ASJ AF: 0.485

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.457

Gnomad4 NFE AF: 0.513

Gnomad4 OTH AF: 0.408

Alfa AF: 0.443 Hom.: 2027

Bravo AF: 0.372

Asia WGS AF: 0.422 AC: 1469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.41
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9332446; hg19: chr10-44516421;