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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372161	XR_935570.3	n.516-2434G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299452	ENST00000763628.1	n.338-2434G>A		intron_variant	Intron 3 of 3
ENSG00000299452	ENST00000763629.1	n.235-2434G>A		intron_variant	Intron 2 of 2
ENSG00000299452	ENST00000763645.1	n.515+3142G>A		intron_variant	Intron 2 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs2061450; hg19: chr18-60760812;