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. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000447709.1(ENSG00000237473):​n.216+27634G>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 ENST00000447709.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630

Genes affected

ENSG00000237473 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000237473	ENST00000447709.1	n.216+27634G>A		intron_variant	Intron 3 of 4	5

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

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.0355

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.242

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.189

Alfa AF: 0.219 Hom.: 3681

Bravo AF: 0.192

Asia WGS AF: 0.0990 AC: 345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2030398; hg19: chr3-173005973;