chr1-247998492-A-G

Position:

• chr1-247998492-A-G

Variant summary

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

The NM_175911.5(OR2L13):​c.-144+61108A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0873 in 152,094 control chromosomes in the GnomAD database, including 744 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 0.087 (744 hom., cov: 32)
• Consequence: OR2L13 NM_175911.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516

Genes affected

OR2L13 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR2L13	NM_001304535.3	c.-19+61108A>G		intron_variant			NP_001291464.1
OR2L13	NM_175911.5	c.-144+61108A>G		intron_variant			NP_787107.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0872 AC: 13257 AN: 151976 Hom.: 741 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.0532

Gnomad ASJ AF: 0.0323

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.0655

Gnomad FIN AF: 0.0298

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0596

Gnomad OTH AF: 0.0804

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

GnomAD4 genome AF: 0.0873 AC: 13273 AN: 152094 Hom.: 744 Cov.: 32 AF XY: 0.0850 AC XY: 6323 AN XY: 74368

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.0531

Gnomad4 ASJ AF: 0.0323

Gnomad4 EAS AF: 0.157

Gnomad4 SAS AF: 0.0643

Gnomad4 FIN AF: 0.0298

Gnomad4 NFE AF: 0.0596

Gnomad4 OTH AF: 0.0805

Alfa AF: 0.0659 Hom.: 178

Bravo AF: 0.0922

Asia WGS AF: 0.0970 AC: 336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.75
DANN	Benign	0.23

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs11590865; hg19: chr1-248161794;