rs17716486

Positions:

• chr19-29272980-C-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, non coding transcript 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: ENST00000657623.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.502

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000657623.1	n.485+3520C>G		intron_variant, non_coding_transcript_variant
	ENST00000663300.1	n.195+3520C>G		intron_variant, non_coding_transcript_variant

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;