rs9311603

Variant names:

• chr3-56493338-A-G
• rs9311603

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.173 AC: 7164 AN: 41526

American (AMR) AF: 0.0655 AC: 1002 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0458 AC: 159 AN: 3470

East Asian (EAS) AF: 0.0991 AC: 514 AN: 5188

South Asian (SAS) AF: 0.0568 AC: 274 AN: 4824

European-Finnish (FIN) AF: 0.0528 AC: 560 AN: 10610

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0874 AC: 5947 AN: 68014

Other (OTH) AF: 0.111 AC: 234 AN: 2116

Alfa AF: 0.0903 Hom.: 978

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
PhyloP100		2.6

Splicing

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

Other links and lift over

dbSNP: rs9311603; hg19: chr3-56527366;