3-30999011-G-T

Variant names:

• chr3-30999011-G-T
• rs1506203
• ENST00000824914.1:n.262+34939C>A

Variant summary

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

The ENST00000824914.1(ENSG00000307279):​n.262+34939C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,082 control chromosomes in the GnomAD database, including 2,076 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 0.15 (2076 hom., cov: 32)
• Consequence: ENSG00000307279 ENST00000824914.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220
• Publications: 5 publications found

Genes affected

ENSG00000307279 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000824914.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000307279	ENST00000824914.1		n.262+34939C>A		intron	N/A
	ENSG00000307279	ENST00000824915.1		n.208+34939C>A		intron	N/A
	ENSG00000307279	ENST00000824916.1		n.58+34939C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23245 AN: 151964 Hom.: 2075 Cov.: 32

Gnomad AFR AF: 0.0780

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.153 AC: 23261 AN: 152082 Hom.: 2076 Cov.: 32 AF XY: 0.155 AC XY: 11527 AN XY: 74338

African (AFR) AF: 0.0780 AC: 3240 AN: 41516

American (AMR) AF: 0.281 AC: 4291 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 487 AN: 3468

East Asian (EAS) AF: 0.303 AC: 1562 AN: 5156

South Asian (SAS) AF: 0.121 AC: 583 AN: 4814

European-Finnish (FIN) AF: 0.120 AC: 1265 AN: 10582

Middle Eastern (MID) AF: 0.161 AC: 47 AN: 292

European-Non Finnish (NFE) AF: 0.166 AC: 11283 AN: 67964

Other (OTH) AF: 0.176 AC: 372 AN: 2108

Alfa AF: 0.125 Hom.: 437

Bravo AF: 0.165

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.0
DANN	Benign	0.36
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs1506203; hg19: chr3-31040503;