chr3-40338-A-G

Variant names:

• chr3-40338-A-G
• rs1516321

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 0.159 in 152,188 control chromosomes in the GnomAD database, including 2,356 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 0.16 (2356 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.533

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.255 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: 0.159 AC: 24184 AN: 152070 Hom.: 2357 Cov.: 32

Gnomad AFR AF: 0.0696

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.0544

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.159 AC: 24196 AN: 152188 Hom.: 2356 Cov.: 32 AF XY: 0.159 AC XY: 11825 AN XY: 74396

Gnomad4 AFR AF: 0.0696

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.264

Gnomad4 EAS AF: 0.0544

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.161

Alfa AF: 0.193 Hom.: 4102

Bravo AF: 0.148

Asia WGS AF: 0.185 AC: 641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.78
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1516321; hg19: chr3-82010;