rs6860577

Variant names:

• chr5-165440015-G-T
• rs6860577
• ENST00000522189.1:n.21+90965G>T

Variant summary

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

The ENST00000522189.1(ENSG00000253693):​n.21+90965G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 152,116 control chromosomes in the GnomAD database, including 8,435 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 0.33 (8435 hom., cov: 33)
• Consequence: ENSG00000253693 ENST00000522189.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.654
• Publications: 1 publications found

Genes affected

ENSG00000253693 (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 = 0.381 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000522189.1. 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
	ENSG00000253693	ENST00000522189.1	TSL:5	n.21+90965G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49801 AN: 151998 Hom.: 8432 Cov.: 33

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.328 AC: 49819 AN: 152116 Hom.: 8435 Cov.: 33 AF XY: 0.324 AC XY: 24117 AN XY: 74388

African (AFR) AF: 0.386 AC: 16011 AN: 41494

American (AMR) AF: 0.284 AC: 4348 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1138 AN: 3466

East Asian (EAS) AF: 0.146 AC: 757 AN: 5172

South Asian (SAS) AF: 0.276 AC: 1329 AN: 4816

European-Finnish (FIN) AF: 0.295 AC: 3128 AN: 10590

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.325 AC: 22088 AN: 67976

Other (OTH) AF: 0.327 AC: 690 AN: 2110

Alfa AF: 0.330 Hom.: 1780

Bravo AF: 0.327

Asia WGS AF: 0.208 AC: 727 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	6.1
DANN	Benign	0.86
PhyloP100		0.65

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: rs6860577;

hg19: chr5-164867020;