3-96744736-A-G

Variant names:

• chr3-96744736-A-G
• rs1395771

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 0.199 in 151,712 control chromosomes in the GnomAD database, including 6,266 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 0.20 (6266 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.653

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.498 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: 0.199 AC: 30144 AN: 151594 Hom.: 6227 Cov.: 32

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.0626

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0256

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.0335

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.199 AC: 30251 AN: 151712 Hom.: 6266 Cov.: 32 AF XY: 0.199 AC XY: 14783 AN XY: 74168

Gnomad4 AFR AF: 0.504

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.0626

Gnomad4 EAS AF: 0.261

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.0256

Gnomad4 NFE AF: 0.0335

Gnomad4 OTH AF: 0.178

Alfa AF: 0.110 Hom.: 374

Bravo AF: 0.238

Asia WGS AF: 0.200 AC: 693 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.48
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1395771; hg19: chr3-96463580;