chr3-30374120-T-G

Variant names:

• chr3-30374120-T-G
• rs4955316
• ENST00000813918.1:n.912T>G

Variant summary

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

The ENST00000813918.1(ENSG00000289450):​n.912T>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 0.138 in 151,848 control chromosomes in the GnomAD database, including 1,806 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 0.14 (1806 hom., cov: 32)
• Consequence: ENSG00000289450 ENST00000813918.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110
• Publications: 6 publications found

Genes affected

ENSG00000289450 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000813918.1. 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
	ENSG00000289450	ENST00000813918.1		n.912T>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000289450	ENST00000684856.2		n.170+963T>G		intron	N/A
	ENSG00000289450	ENST00000688998.3		n.190+963T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20912 AN: 151730 Hom.: 1797 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.0585

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0858

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.138 AC: 20942 AN: 151848 Hom.: 1806 Cov.: 32 AF XY: 0.142 AC XY: 10520 AN XY: 74188

African (AFR) AF: 0.174 AC: 7221 AN: 41420

American (AMR) AF: 0.266 AC: 4055 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.0585 AC: 203 AN: 3470

East Asian (EAS) AF: 0.236 AC: 1210 AN: 5128

South Asian (SAS) AF: 0.170 AC: 817 AN: 4818

European-Finnish (FIN) AF: 0.116 AC: 1220 AN: 10562

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0857 AC: 5822 AN: 67906

Other (OTH) AF: 0.121 AC: 254 AN: 2100

Alfa AF: 0.125 Hom.: 1344

Bravo AF: 0.155

Asia WGS AF: 0.212 AC: 738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.3
DANN	Benign	0.49
PhyloP100		0.011

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: rs4955316;

hg19: chr3-30415612;