rs1859524

Variant names:

• chr7-47000577-G-A
• rs1859524
• ENST00000423781.2:n.379-25560G>A

Variant summary

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

The ENST00000423781.2(ENSG00000223829):​n.379-25560G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 152,048 control chromosomes in the GnomAD database, including 8,529 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 0.32 (8529 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000223829 ENST00000423781.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.397
• Publications: 2 publications found

Genes affected

ENSG00000223829 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000423781.2. 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
	ENSG00000223829	ENST00000423781.2	TSL:3	n.379-25560G>A		intron	N/A
	ENSG00000232072	ENST00000433337.1	TSL:3	n.237+48865C>T		intron	N/A
	ENSG00000223829	ENST00000740061.1		n.680+18274G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48582 AN: 151930 Hom.: 8536 Cov.: 33

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.341

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.320 AC: 48584 AN: 152048 Hom.: 8529 Cov.: 33 AF XY: 0.314 AC XY: 23312 AN XY: 74304

African (AFR) AF: 0.186 AC: 7711 AN: 41514

American (AMR) AF: 0.376 AC: 5742 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1220 AN: 3468

East Asian (EAS) AF: 0.244 AC: 1264 AN: 5172

South Asian (SAS) AF: 0.437 AC: 2102 AN: 4810

European-Finnish (FIN) AF: 0.231 AC: 2434 AN: 10554

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.398 AC: 27020 AN: 67948

Other (OTH) AF: 0.341 AC: 720 AN: 2112

Alfa AF: 0.380 Hom.: 19263

Bravo AF: 0.320

Asia WGS AF: 0.337 AC: 1175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.4
DANN	Benign	0.54
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs1859524; hg19: chr7-47040175;