3-96744736-A-G

Variant names:

• chr3-96744736-A-G
• rs1395771

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 0.199 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.504 AC: 20834 AN: 41352

American (AMR) AF: 0.289 AC: 4378 AN: 15174

Ashkenazi Jewish (ASJ) AF: 0.0626 AC: 217 AN: 3466

East Asian (EAS) AF: 0.261 AC: 1343 AN: 5152

South Asian (SAS) AF: 0.110 AC: 531 AN: 4830

European-Finnish (FIN) AF: 0.0256 AC: 272 AN: 10610

Middle Eastern (MID) AF: 0.0925 AC: 27 AN: 292

European-Non Finnish (NFE) AF: 0.0335 AC: 2273 AN: 67820

Other (OTH) AF: 0.178 AC: 375 AN: 2104

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.48
DANN	Benign	0.48
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs1395771; hg19: chr3-96463580;