rs6042588

Variant names:

• chr20-1492751-A-G
• rs6042588
• ENST00000824325.1:n.238+951A>G

Variant summary

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

The ENST00000824325.1(ENSG00000307156):​n.238+951A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,160 control chromosomes in the GnomAD database, including 4,875 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 0.19 (4875 hom., cov: 32)
• Consequence: ENSG00000307156 ENST00000824325.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970
• Publications: 7 publications found

Genes affected

ENSG00000307156 (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 = 0.441 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
ENSG00000307156	ENST00000824325.1	n.238+951A>G		intron_variant	Intron 1 of 1
ENSG00000307156	ENST00000824326.1	n.92+200A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29595 AN: 152042 Hom.: 4870 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.0834

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0967

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.195 AC: 29645 AN: 152160 Hom.: 4875 Cov.: 32 AF XY: 0.191 AC XY: 14182 AN XY: 74400

African (AFR) AF: 0.447 AC: 18532 AN: 41470

American (AMR) AF: 0.120 AC: 1841 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 519 AN: 3472

East Asian (EAS) AF: 0.00270 AC: 14 AN: 5184

South Asian (SAS) AF: 0.150 AC: 722 AN: 4822

European-Finnish (FIN) AF: 0.0834 AC: 884 AN: 10598

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0968 AC: 6580 AN: 68006

Other (OTH) AF: 0.176 AC: 372 AN: 2112

Alfa AF: 0.161 Hom.: 583

Bravo AF: 0.207

Asia WGS AF: 0.0840 AC: 295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.2
DANN	Benign	0.64
PhyloP100		-0.097

Splicing

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

Other links and lift over

dbSNP: rs6042588; hg19: chr20-1473397;