rs9311603

Positions:

• chr3-56493338-A-G

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 0.105 in 152,240 control chromosomes in the GnomAD database, including 1,001 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 0.10 (1001 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.64

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15920 AN: 152122 Hom.: 994 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.0846

Gnomad AMR AF: 0.0658

Gnomad ASJ AF: 0.0458

Gnomad EAS AF: 0.0988

Gnomad SAS AF: 0.0565

Gnomad FIN AF: 0.0528

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0874

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.105 AC: 15958 AN: 152240 Hom.: 1001 Cov.: 32 AF XY: 0.101 AC XY: 7554 AN XY: 74442

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.0655

Gnomad4 ASJ AF: 0.0458

Gnomad4 EAS AF: 0.0991

Gnomad4 SAS AF: 0.0568

Gnomad4 FIN AF: 0.0528

Gnomad4 NFE AF: 0.0874

Gnomad4 OTH AF: 0.111

Alfa AF: 0.0903 Hom.: 646

Bravo AF: 0.111

Asia WGS AF: 0.0770 AC: 268 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.7
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9311603; hg19: chr3-56527366;