rs4318565

Variant names:

• chr3-96362666-T-C
• rs4318565

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 0.0421 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0447 AC: 1858 AN: 41568

American (AMR) AF: 0.0234 AC: 357 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0412 AC: 143 AN: 3470

East Asian (EAS) AF: 0.0454 AC: 235 AN: 5178

South Asian (SAS) AF: 0.123 AC: 596 AN: 4830

European-Finnish (FIN) AF: 0.0414 AC: 439 AN: 10592

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0388 AC: 2641 AN: 67986

Other (OTH) AF: 0.0341 AC: 72 AN: 2114

Alfa AF: 0.0369 Hom.: 44

Bravo AF: 0.0393

Asia WGS AF: 0.0840 AC: 296 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.70
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs4318565; hg19: chr3-96081510;