rs2169520

Variant names:

• chr5-63302626-T-C
• rs2169520
• ENST00000823418.1:n.286+582T>C

Variant summary

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

The ENST00000823418.1(ENSG00000307084):​n.286+582T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,086 control chromosomes in the GnomAD database, including 5,260 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 0.24 (5260 hom., cov: 32)
• Consequence: ENSG00000307084 ENST00000823418.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.417
• Publications: 6 publications found

Genes affected

ENSG00000307084 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000823418.1. 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
	ENSG00000307084	ENST00000823418.1		n.286+582T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37157 AN: 151968 Hom.: 5250 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.245 AC: 37190 AN: 152086 Hom.: 5260 Cov.: 32 AF XY: 0.236 AC XY: 17542 AN XY: 74352

African (AFR) AF: 0.387 AC: 16061 AN: 41448

American (AMR) AF: 0.212 AC: 3236 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 777 AN: 3470

East Asian (EAS) AF: 0.138 AC: 714 AN: 5178

South Asian (SAS) AF: 0.101 AC: 487 AN: 4826

European-Finnish (FIN) AF: 0.102 AC: 1077 AN: 10606

Middle Eastern (MID) AF: 0.397 AC: 116 AN: 292

European-Non Finnish (NFE) AF: 0.206 AC: 14010 AN: 67988

Other (OTH) AF: 0.264 AC: 557 AN: 2112

Alfa AF: 0.223 Hom.: 6712

Bravo AF: 0.264

Asia WGS AF: 0.130 AC: 455 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.3
DANN	Benign	0.78
PhyloP100		-0.42

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: rs2169520;

hg19: chr5-62598453;