rs688187

Variant names:

• chr19-39242112-G-A
• rs688187
• ENST00000735578.1:n.116-1124G>A

Variant summary

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

The ENST00000735578.1(ENSG00000296032):​n.116-1124G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 150,696 control chromosomes in the GnomAD database, including 12,992 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 0.39 (12992 hom., cov: 31)
• Consequence: ENSG00000296032 ENST00000735578.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.342
• Publications: 23 publications found

Genes affected

ENSG00000296032 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000735578.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296032	ENST00000735578.1		n.116-1124G>A		intron	N/A
	ENSG00000296032	ENST00000735579.1		n.90-1124G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58199 AN: 150580 Hom.: 12960 Cov.: 31

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.0711

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.387 AC: 58279 AN: 150696 Hom.: 12992 Cov.: 31 AF XY: 0.377 AC XY: 27743 AN XY: 73628

African (AFR) AF: 0.606 AC: 24714 AN: 40776

American (AMR) AF: 0.372 AC: 5652 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1342 AN: 3456

East Asian (EAS) AF: 0.0715 AC: 370 AN: 5176

South Asian (SAS) AF: 0.218 AC: 1038 AN: 4766

European-Finnish (FIN) AF: 0.238 AC: 2507 AN: 10520

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.318 AC: 21469 AN: 67534

Other (OTH) AF: 0.359 AC: 750 AN: 2088

Alfa AF: 0.372 Hom.: 1373

Bravo AF: 0.409

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.71
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs688187; hg19: chr19-39732752;