rs2502389

Variant names:

• chr6-113146970-C-T
• rs2502389
• ENST00000722487.1:n.139+20117C>T

Variant summary

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

The ENST00000722487.1(ENSG00000287728):​n.139+20117C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 152,024 control chromosomes in the GnomAD database, including 16,471 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 0.46 (16471 hom., cov: 32)
• Consequence: ENSG00000287728 ENST00000722487.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.886
• Publications: 0 publications found

Genes affected

ENSG00000287728 (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 = 0.575 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000722487.1. 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
	ENSG00000287728	ENST00000722487.1		n.139+20117C>T		intron	N/A
	ENSG00000287728	ENST00000722488.1		n.436+9175C>T		intron	N/A
	ENSG00000287728	ENST00000722489.1		n.82+20122C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69425 AN: 151906 Hom.: 16452 Cov.: 32

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.457 AC: 69497 AN: 152024 Hom.: 16471 Cov.: 32 AF XY: 0.459 AC XY: 34103 AN XY: 74292

African (AFR) AF: 0.581 AC: 24081 AN: 41468

American (AMR) AF: 0.422 AC: 6431 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1581 AN: 3470

East Asian (EAS) AF: 0.483 AC: 2497 AN: 5170

South Asian (SAS) AF: 0.329 AC: 1589 AN: 4824

European-Finnish (FIN) AF: 0.489 AC: 5164 AN: 10568

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.395 AC: 26840 AN: 67948

Other (OTH) AF: 0.454 AC: 960 AN: 2114

Alfa AF: 0.404 Hom.: 6594

Bravo AF: 0.463

Asia WGS AF: 0.398 AC: 1384 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	0.048
DANN	Benign	0.27
PhyloP100		-0.89

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2502389; hg19: chr6-113468172; COSMIC: COSV68646779;