3-112307273-A-G

Variant names:

• chr3-112307273-A-G
• rs6773206
• ENST00000498032.5:n.237+4559A>G

Variant summary

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

The ENST00000498032.5(ENSG00000239482):​n.237+4559A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 152,054 control chromosomes in the GnomAD database, including 13,742 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 0.43 (13742 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000239482 ENST00000498032.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 1 publications found

Genes affected

ENSG00000239482 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374042	NR_147411.1	n.237+4559A>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000239482	ENST00000498032.5	n.237+4559A>G		intron_variant	Intron 1 of 4	1
ENSG00000239482	ENST00000607456.1	n.78+75A>G		intron_variant	Intron 1 of 4	5
ENSG00000239482	ENST00000793967.1	n.*38A>G		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64707 AN: 151936 Hom.: 13745 Cov.: 32

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.452

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.426 AC: 64736 AN: 152054 Hom.: 13742 Cov.: 32 AF XY: 0.423 AC XY: 31430 AN XY: 74322

African (AFR) AF: 0.416 AC: 17239 AN: 41448

American (AMR) AF: 0.408 AC: 6237 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1456 AN: 3470

East Asian (EAS) AF: 0.461 AC: 2386 AN: 5174

South Asian (SAS) AF: 0.451 AC: 2169 AN: 4812

European-Finnish (FIN) AF: 0.415 AC: 4386 AN: 10560

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.432 AC: 29381 AN: 67980

Other (OTH) AF: 0.456 AC: 962 AN: 2108

Alfa AF: 0.427 Hom.: 59330

Bravo AF: 0.427

Asia WGS AF: 0.490 AC: 1701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	8.1
DANN	Benign	0.95
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs6773206; hg19: chr3-112026120;