rs3739821

Positions:

• chr9-127940198-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000592240.5(ENSG00000227218):​n.144-209A>G variant causes a intron, non coding transcript 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: ENST00000592240.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC124902280	XR_007061801.1	n.317-209A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000592240.5	n.144-209A>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.667

Gnomad4 OTH exome AF: 1.00

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

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.692

Gnomad4 ASJ AF: 0.608

Gnomad4 EAS AF: 0.258

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.779

Gnomad4 NFE AF: 0.774

Gnomad4 OTH AF: 0.611

Alfa AF: 0.730 Hom.: 81794

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3739821; hg19: chr9-130702477;