3-96362666-T-C

Position:

• chr3-96362666-T-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 0.0421 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;