3-30299934-A-G

Position:

• chr3-30299934-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000659869.1(ENSG00000287774):​n.236+1034A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 151,988 control chromosomes in the GnomAD database, including 15,247 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 0.42 (15247 hom., cov: 33)
• Consequence: ENSG00000287774 ENST00000659869.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.56

Genes affected

ENSG00000287774 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124909358	XR_007095854.1	n.110-4384A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287774	ENST00000659869.1	n.236+1034A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64521 AN: 151870 Hom.: 15227 Cov.: 33

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.425 AC: 64585 AN: 151988 Hom.: 15247 Cov.: 33 AF XY: 0.428 AC XY: 31761 AN XY: 74280

Gnomad4 AFR AF: 0.640

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.428

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.338

Gnomad4 OTH AF: 0.379

Alfa AF: 0.347 Hom.: 18950

Bravo AF: 0.421

Asia WGS AF: 0.417 AC: 1453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0050
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9819616; hg19: chr3-30341425;