rs2097063

Variant names:

• chr18-73963859-T-C
• rs2097063
• ENST00000581541.1:n.122-48830A>G

Variant summary

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

The ENST00000581541.1(ENSG00000263655):​n.122-48830A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 152,066 control chromosomes in the GnomAD database, including 2,833 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 0.18 (2833 hom., cov: 32)
• Consequence: ENSG00000263655 ENST00000581541.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

Genes affected

ENSG00000263655 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000263655	ENST00000581541.1	n.122-48830A>G		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28053 AN: 151948 Hom.: 2834 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0642

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.185 AC: 28062 AN: 152066 Hom.: 2833 Cov.: 32 AF XY: 0.180 AC XY: 13362 AN XY: 74336

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.0644

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.185

Alfa AF: 0.194 Hom.: 335

Bravo AF: 0.186

Asia WGS AF: 0.0480 AC: 169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.0
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2097063; hg19: chr18-71631094;