3-30299934-A-G

Variant names:

• chr3-30299934-A-G
• rs9819616
• ENST00000810629.1:n.796A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000810629.1(ENSG00000287774):​n.796A>G variant causes a non coding transcript exon 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 ENST00000810629.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.56
• Publications: 4 publications found

Genes affected

ENSG00000287774 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000810629.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287774	ENST00000810629.1		n.796A>G		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000287774	ENST00000810630.1		n.738A>G		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000287774	ENST00000810631.1		n.646A>G		non_coding_transcript_exon	Exon 3 of 3

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

African (AFR) AF: 0.640 AC: 26531 AN: 41456

American (AMR) AF: 0.284 AC: 4336 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1127 AN: 3472

East Asian (EAS) AF: 0.428 AC: 2206 AN: 5160

South Asian (SAS) AF: 0.354 AC: 1708 AN: 4820

European-Finnish (FIN) AF: 0.427 AC: 4507 AN: 10552

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.338 AC: 22953 AN: 67962

Other (OTH) AF: 0.379 AC: 799 AN: 2110

Alfa AF: 0.364 Hom.: 35101

Bravo AF: 0.421

Asia WGS AF: 0.417 AC: 1453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0050
DANN	Benign	0.34
PhyloP100		-3.6

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9819616;

hg19: chr3-30341425;