rs935053

Variant names:

• chr9-21783923-G-A
• rs935053

Your query was ambiguous. Multiple possible variants found:

• chr9-21783923-G-A
• chr9-21783923-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 0.615 in 151,034 control chromosomes in the GnomAD database, including 29,740 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 (29740 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.287

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.805 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: 0.614 AC: 92705 AN: 150926 Hom.: 29675 Cov.: 28

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.615 AC: 92836 AN: 151034 Hom.: 29740 Cov.: 28 AF XY: 0.610 AC XY: 45000 AN XY: 73744

Gnomad4 AFR AF: 0.812

Gnomad4 AMR AF: 0.603

Gnomad4 ASJ AF: 0.551

Gnomad4 EAS AF: 0.710

Gnomad4 SAS AF: 0.428

Gnomad4 FIN AF: 0.525

Gnomad4 NFE AF: 0.524

Gnomad4 OTH AF: 0.582

Alfa AF: 0.580 Hom.: 3074

Bravo AF: 0.636

Asia WGS AF: 0.581 AC: 2020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.62
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs935053; hg19: chr9-21783922;