rs679582

Variant names:

• chr6-139510043-G-A
• rs679582
• ENST00000647815.1:n.134+23428G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000647815.1(ENSG00000226571):​n.134+23428G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 151,954 control chromosomes in the GnomAD database, including 24,406 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 0.56 (24406 hom., cov: 32)
• Consequence: ENSG00000226571 ENST00000647815.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.784

Genes affected

ENSG00000226571 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.693 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+23428G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.560 AC: 84984 AN: 151836 Hom.: 24384 Cov.: 32

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.560 AC: 85053 AN: 151954 Hom.: 24406 Cov.: 32 AF XY: 0.560 AC XY: 41563 AN XY: 74280

Gnomad4 AFR AF: 0.453

Gnomad4 AMR AF: 0.582

Gnomad4 ASJ AF: 0.661

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.713

Gnomad4 FIN AF: 0.547

Gnomad4 NFE AF: 0.623

Gnomad4 OTH AF: 0.578

Alfa AF: 0.585 Hom.: 3521

Bravo AF: 0.552

Asia WGS AF: 0.533 AC: 1853 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	0.12
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs679582; hg19: chr6-139831180; COSMIC: COSV69428605;