rs4128725

chr1-159436169-T-Cchr1-159436169-T-G

Variant summary

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

The ENST00000431862.1(ENSG00000228560):n.227+32673A>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 0.108 in 152,048 control chromosomes in the GnomAD database, including 1,142 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 0.11 (1142 hom., cov: 31)
• Consequence: ENST00000431862.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.522

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR10J1	NM_001363557.2	c.-16-3607T>C		intron_variant
OR10J1	NM_001363558.2	c.-16-3607T>C		intron_variant
OR10J1	XM_047417793.1	c.-16-3607T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000431862.1	n.227+32673A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16430 AN: 151932 Hom.: 1142 Cov.: 31

Gnomad AFR AF: 0.0391

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.108 AC: 16428 AN: 152048 Hom.: 1142 Cov.: 31 AF XY: 0.110 AC XY: 8213 AN XY: 74330

Gnomad4 AFR AF: 0.0390

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.230

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.115

Alfa AF: 0.112 Hom.: 1285

Bravo AF: 0.114

Asia WGS AF: 0.219 AC: 760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	5.5
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4128725; hg19: chr1-159405959;