rs2030398

Variant names:

• chr3-173288183-G-A
• rs2030398
• ENST00000447709.1:n.216+27634G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-173288183-G-A
• chr3-173288183-G-C
• chr3-173288183-G-T

Variant summary

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

The ENST00000762920.1(ENSG00000237473):​n.221+28370G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 152,128 control chromosomes in the GnomAD database, including 3,236 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 0.20 (3236 hom., cov: 32)
• Consequence: ENSG00000237473 ENST00000762920.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630
• Publications: 3 publications found

Genes affected

ENSG00000237473 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762920.1. 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
	ENSG00000237473	ENST00000447709.1	TSL:5	n.216+27634G>A		intron	N/A
	ENSG00000237473	ENST00000762920.1		n.221+28370G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30471 AN: 152010 Hom.: 3231 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.0354

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.200 AC: 30484 AN: 152128 Hom.: 3236 Cov.: 32 AF XY: 0.197 AC XY: 14619 AN XY: 74378

African (AFR) AF: 0.166 AC: 6877 AN: 41484

American (AMR) AF: 0.184 AC: 2812 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 716 AN: 3470

East Asian (EAS) AF: 0.0355 AC: 184 AN: 5182

South Asian (SAS) AF: 0.122 AC: 591 AN: 4828

European-Finnish (FIN) AF: 0.242 AC: 2558 AN: 10578

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16155 AN: 67986

Other (OTH) AF: 0.189 AC: 399 AN: 2110

Alfa AF: 0.216 Hom.: 4515

Bravo AF: 0.192

Asia WGS AF: 0.0990 AC: 345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.70
DANN	Benign	0.27
PhyloP100		-0.063

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: rs2030398;

hg19: chr3-173005973;