rs6050372

Variant names:

• chr20-25152589-A-G
• rs6050372
• ENST00000830986.1:n.489+7704T>C

Variant summary

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

The ENST00000830986.1(ENSG00000230725):​n.489+7704T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 151,768 control chromosomes in the GnomAD database, including 14,902 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 0.41 (14902 hom., cov: 31)
• Consequence: ENSG00000230725 ENST00000830986.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.39
• Publications: 9 publications found

Genes affected

ENSG00000230725 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230725	ENST00000830986.1	n.489+7704T>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61565 AN: 151650 Hom.: 14869 Cov.: 31

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.406 AC: 61649 AN: 151768 Hom.: 14902 Cov.: 31 AF XY: 0.405 AC XY: 30033 AN XY: 74142

African (AFR) AF: 0.671 AC: 27728 AN: 41322

American (AMR) AF: 0.424 AC: 6470 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1405 AN: 3464

East Asian (EAS) AF: 0.427 AC: 2196 AN: 5142

South Asian (SAS) AF: 0.361 AC: 1734 AN: 4802

European-Finnish (FIN) AF: 0.273 AC: 2880 AN: 10546

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18093 AN: 67936

Other (OTH) AF: 0.383 AC: 808 AN: 2112

Alfa AF: 0.313 Hom.: 4417

Bravo AF: 0.430

Asia WGS AF: 0.443 AC: 1536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.16
DANN	Benign	0.26
PhyloP100		-3.4

Splicing

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

Other links and lift over

dbSNP: rs6050372; hg19: chr20-25133225;