rs2061450

Variant names:

• chr18-63093579-G-A
• rs2061450
• ENST00000763628.1:n.338-2434G>A

Your query was ambiguous. Multiple possible variants found:

• chr18-63093579-G-A
• chr18-63093579-G-T

Variant summary

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

The ENST00000763628.1(ENSG00000299452):​n.338-2434G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,014 control chromosomes in the GnomAD database, including 6,604 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 0.28 (6604 hom., cov: 32)
• Consequence: ENSG00000299452 ENST00000763628.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 2 publications found

Genes affected

ENSG00000299452 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000763628.1. 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
	ENSG00000299452	ENST00000763628.1		n.338-2434G>A		intron	N/A
	ENSG00000299452	ENST00000763629.1		n.235-2434G>A		intron	N/A
	ENSG00000299452	ENST00000763645.1		n.515+3142G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43197 AN: 151896 Hom.: 6595 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.285 AC: 43250 AN: 152014 Hom.: 6604 Cov.: 32 AF XY: 0.288 AC XY: 21366 AN XY: 74316

African (AFR) AF: 0.317 AC: 13144 AN: 41452

American (AMR) AF: 0.364 AC: 5564 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 801 AN: 3470

East Asian (EAS) AF: 0.489 AC: 2526 AN: 5170

South Asian (SAS) AF: 0.381 AC: 1834 AN: 4812

European-Finnish (FIN) AF: 0.218 AC: 2302 AN: 10568

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16129 AN: 67954

Other (OTH) AF: 0.255 AC: 538 AN: 2112

Alfa AF: 0.232 Hom.: 2273

Bravo AF: 0.298

Asia WGS AF: 0.413 AC: 1434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.19
DANN	Benign	0.80
PhyloP100		-1.4

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: rs2061450;

hg19: chr18-60760812;