rs409228

Variant names:

• chr3-41023922-G-T
• rs409228
• ENST00000822540.1:n.973C>A

Variant summary

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

The ENST00000822540.1(ENSG00000307002):​n.973C>A 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 0.333 in 152,002 control chromosomes in the GnomAD database, including 8,918 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 0.33 (8918 hom., cov: 32)
• Consequence: ENSG00000307002 ENST00000822540.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.494
• Publications: 3 publications found

Genes affected

ENSG00000307002 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000822540.1. 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
	ENSG00000307002	ENST00000822540.1		n.973C>A		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50527 AN: 151884 Hom.: 8886 Cov.: 32

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.333 AC: 50605 AN: 152002 Hom.: 8918 Cov.: 32 AF XY: 0.328 AC XY: 24367 AN XY: 74320

African (AFR) AF: 0.435 AC: 18039 AN: 41422

American (AMR) AF: 0.366 AC: 5600 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1629 AN: 3464

East Asian (EAS) AF: 0.236 AC: 1216 AN: 5150

South Asian (SAS) AF: 0.303 AC: 1459 AN: 4810

European-Finnish (FIN) AF: 0.226 AC: 2393 AN: 10574

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.283 AC: 19230 AN: 67976

Other (OTH) AF: 0.320 AC: 676 AN: 2110

Alfa AF: 0.304 Hom.: 14273

Bravo AF: 0.349

Asia WGS AF: 0.314 AC: 1092 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.72
PhyloP100		-0.49

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: rs409228;

hg19: chr3-41065413;