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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902280	XR_007061801.1	n.317-209A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227218	ENST00000415141.2	n.463A>G		non_coding_transcript_exon_variant	Exon 1 of 2	2
ENSG00000227218	ENST00000586374.5	n.363-209A>G		intron_variant	Intron 1 of 2	5
ENSG00000227218	ENST00000587355.5	n.498-209A>G		intron_variant	Intron 2 of 3	5

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 v4.3

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

Other links and lift over

dbSNP: rs3739821; hg19: chr9-130702477;