rs592423

Variant names:

• chr6-139519556-A-C
• rs592423
• ENST00000647815.1:n.134+32941A>C

Variant summary

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

The ENST00000647815.1(ENSG00000226571):​n.134+32941A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 152,026 control chromosomes in the GnomAD database, including 19,427 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 0.50 (19427 hom., cov: 31)
• Consequence: ENSG00000226571 ENST00000647815.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.247
• Publications: 32 publications found

Genes affected

ENSG00000226571 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.651 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
ENSG00000226571	ENST00000647815.1	n.134+32941A>C		intron_variant	Intron 1 of 2
ENSG00000226571	ENST00000775574.1	n.194-27686A>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75783 AN: 151908 Hom.: 19400 Cov.: 31

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.499 AC: 75847 AN: 152026 Hom.: 19427 Cov.: 31 AF XY: 0.499 AC XY: 37100 AN XY: 74322

African (AFR) AF: 0.397 AC: 16469 AN: 41448

American (AMR) AF: 0.543 AC: 8300 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2116 AN: 3472

East Asian (EAS) AF: 0.273 AC: 1411 AN: 5170

South Asian (SAS) AF: 0.670 AC: 3229 AN: 4820

European-Finnish (FIN) AF: 0.474 AC: 4996 AN: 10550

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.553 AC: 37555 AN: 67968

Other (OTH) AF: 0.520 AC: 1098 AN: 2112

Alfa AF: 0.529 Hom.: 60187

Bravo AF: 0.493

Asia WGS AF: 0.496 AC: 1725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.34
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs592423; hg19: chr6-139840693;