rs4318565

Variant names:

• chr3-96362666-T-C
• rs4318565

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 0.0421 in 152,224 control chromosomes in the GnomAD database, including 157 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 0.042 (157 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.976

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 = 0.115 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: 0.0421 AC: 6399 AN: 152106 Hom.: 154 Cov.: 32

Gnomad AFR AF: 0.0445

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0234

Gnomad ASJ AF: 0.0412

Gnomad EAS AF: 0.0455

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0414

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0389

Gnomad OTH AF: 0.0344

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

GnomAD4 genome AF: 0.0421 AC: 6414 AN: 152224 Hom.: 157 Cov.: 32 AF XY: 0.0431 AC XY: 3206 AN XY: 74424

Gnomad4 AFR AF: 0.0447

Gnomad4 AMR AF: 0.0234

Gnomad4 ASJ AF: 0.0412

Gnomad4 EAS AF: 0.0454

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.0414

Gnomad4 NFE AF: 0.0388

Gnomad4 OTH AF: 0.0341

Alfa AF: 0.0368 Hom.: 34

Bravo AF: 0.0393

Asia WGS AF: 0.0840 AC: 296 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4318565; hg19: chr3-96081510;