rs9310704

Positions:

• chr3-22669955-G-A
• chr3-22669955-G-C

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 0.609 in 152,018 control chromosomes in the GnomAD database, including 28,270 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 (28270 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.576

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.657 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: 0.609 AC: 92488 AN: 151900 Hom.: 28272 Cov.: 32

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.609 AC: 92525 AN: 152018 Hom.: 28270 Cov.: 32 AF XY: 0.608 AC XY: 45177 AN XY: 74314

Gnomad4 AFR AF: 0.597

Gnomad4 AMR AF: 0.619

Gnomad4 ASJ AF: 0.530

Gnomad4 EAS AF: 0.610

Gnomad4 SAS AF: 0.677

Gnomad4 FIN AF: 0.555

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.601

Alfa AF: 0.615 Hom.: 12691

Bravo AF: 0.610

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.3
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9310704; hg19: chr3-22711446;