rs935053

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;