rs2097063

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

ENSG00000263655 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000581541.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000263655	ENST00000581541.1	TSL:3	n.122-48830A>G		intron	N/A
	ENSG00000287314	ENST00000753825.1		n.543+15508T>C		intron	N/A

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

African (AFR) AF: 0.196 AC: 8109 AN: 41468

American (AMR) AF: 0.147 AC: 2247 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 811 AN: 3468

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5184

South Asian (SAS) AF: 0.0644 AC: 310 AN: 4810

European-Finnish (FIN) AF: 0.202 AC: 2135 AN: 10560

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.204 AC: 13839 AN: 67972

Other (OTH) AF: 0.185 AC: 391 AN: 2114

Alfa AF: 0.193 Hom.: 346

Bravo AF: 0.186

Asia WGS AF: 0.0480 AC: 169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.0
DANN	Benign	0.66
PhyloP100		0.31

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2097063;

hg19: chr18-71631094;