chr19-29272980-C-G

Variant names:

• chr19-29272980-C-G
• rs17716486
• ENST00000657623.1:n.485+3520C>G

Variant summary

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

The ENST00000657623.1(ENSG00000287272):​n.485+3520C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 152,120 control chromosomes in the GnomAD database, including 2,736 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 0.18 (2736 hom., cov: 33)
• Consequence: ENSG00000287272 ENST00000657623.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.502

Genes affected

ENSG00000287272 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.331 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
ENSG00000287272	ENST00000657623.1	n.485+3520C>G		intron_variant	Intron 1 of 2
ENSG00000287272	ENST00000663300.1	n.195+3520C>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.184 AC: 27971 AN: 152002 Hom.: 2731 Cov.: 33

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.184 AC: 28001 AN: 152120 Hom.: 2736 Cov.: 33 AF XY: 0.189 AC XY: 14054 AN XY: 74362

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.190

Alfa AF: 0.158 Hom.: 263

Bravo AF: 0.184

Asia WGS AF: 0.334 AC: 1162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.4
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17716486; hg19: chr19-29763887;