rs3739821

Variant names:

• chr9-127940198-A-G
• rs3739821
• ENST00000415141.2:n.463A>G

Variant summary

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

The ENST00000415141.2(ENSG00000227218):​n.463A>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 0.604 in 152,180 control chromosomes in the GnomAD database, including 31,264 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 0.60 (31262 hom., cov: 33)
  • Exomes 𝑓: 0.70 (2 hom.)
• Consequence: ENSG00000227218 ENST00000415141.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 27 publications found

Genes affected

ENSG00000227218 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000415141.2. 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
	ENSG00000227218	ENST00000415141.2	TSL:2	n.463A>G		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000227218	ENST00000586374.5	TSL:5	n.363-209A>G		intron	N/A
	ENSG00000227218	ENST00000587355.5	TSL:5	n.498-209A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.605 AC: 91918 AN: 152052 Hom.: 31252 Cov.: 33

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.611

GnomAD4 exome AF: 0.700 AC: 7 AN: 10 Hom.: 2 Cov.: 0 AF XY: 0.750 AC XY: 3 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.667 AC: 4 AN: 6

Other (OTH) AF: 1.00 AC: 2 AN: 2

GnomAD4 genome AF: 0.604 AC: 91947 AN: 152170 Hom.: 31262 Cov.: 33 AF XY: 0.602 AC XY: 44826 AN XY: 74402

African (AFR) AF: 0.305 AC: 12669 AN: 41500

American (AMR) AF: 0.692 AC: 10585 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2107 AN: 3468

East Asian (EAS) AF: 0.258 AC: 1335 AN: 5172

South Asian (SAS) AF: 0.452 AC: 2182 AN: 4824

European-Finnish (FIN) AF: 0.779 AC: 8248 AN: 10594

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.774 AC: 52613 AN: 68004

Other (OTH) AF: 0.611 AC: 1291 AN: 2112

Alfa AF: 0.711 Hom.: 168571

Bravo AF: 0.587

Asia WGS AF: 0.406 AC: 1415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.58
DANN	Benign	0.68
PhyloP100		-1.3

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: rs3739821;

hg19: chr9-130702477;