3-30499934-A-G

Position:

• chr3-30499934-A-G

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 0.313 in 151,952 control chromosomes in the GnomAD database, including 7,744 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 0.31 (7744 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 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: 0.313 AC: 47589 AN: 151834 Hom.: 7741 Cov.: 32

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.313 AC: 47618 AN: 151952 Hom.: 7744 Cov.: 32 AF XY: 0.313 AC XY: 23257 AN XY: 74274

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.328

Alfa AF: 0.306 Hom.: 1051

Bravo AF: 0.312

Asia WGS AF: 0.346 AC: 1202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7644410; hg19: chr3-30541426;