rs2248461

Variant names:

• chr20-54175663-G-A
• rs2248461
• ENST00000655028.2:n.569+734G>A

Your query was ambiguous. Multiple possible variants found:

• chr20-54175663-G-A
• chr20-54175663-G-C
• chr20-54175663-G-T

Variant summary

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

The ENST00000655028.2(ENSG00000286587):​n.569+734G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 151,982 control chromosomes in the GnomAD database, including 16,347 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 0.45 (16347 hom., cov: 32)
• Consequence: ENSG00000286587 ENST00000655028.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610
• Publications: 12 publications found

Genes affected

ENSG00000286587 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000655028.2. 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
	ENSG00000286587	ENST00000655028.2		n.569+734G>A		intron	N/A
	ENSG00000286587	ENST00000792273.1		n.288+7092G>A		intron	N/A
	ENSG00000286587	ENST00000792274.1		n.279-2729G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.448 AC: 67976 AN: 151864 Hom.: 16301 Cov.: 32

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.448 AC: 68078 AN: 151982 Hom.: 16347 Cov.: 32 AF XY: 0.444 AC XY: 32980 AN XY: 74320

African (AFR) AF: 0.640 AC: 26501 AN: 41416

American (AMR) AF: 0.349 AC: 5328 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1918 AN: 3470

East Asian (EAS) AF: 0.359 AC: 1856 AN: 5174

South Asian (SAS) AF: 0.407 AC: 1962 AN: 4822

European-Finnish (FIN) AF: 0.333 AC: 3521 AN: 10562

Middle Eastern (MID) AF: 0.459 AC: 134 AN: 292

European-Non Finnish (NFE) AF: 0.376 AC: 25551 AN: 67964

Other (OTH) AF: 0.460 AC: 971 AN: 2110

Alfa AF: 0.406 Hom.: 35781

Bravo AF: 0.455

Asia WGS AF: 0.409 AC: 1419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.86
DANN	Benign	0.61
PhyloP100		-0.061

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: rs2248461;

hg19: chr20-52792202;