rs1019156

Variant names:

• chr17-14671327-A-G
• rs1019156

Variant summary

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

The variant allele was found at a frequency of 0.126 in 152,212 control chromosomes in the GnomAD database, including 1,607 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 0.13 (1607 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.217 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

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19095 AN: 152094 Hom.: 1600 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.0519

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0777

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.126 AC: 19114 AN: 152212 Hom.: 1607 Cov.: 32 AF XY: 0.125 AC XY: 9293 AN XY: 74398

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.0513

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.0777

Gnomad4 OTH AF: 0.112

Alfa AF: 0.0924 Hom.: 480

Bravo AF: 0.134

Asia WGS AF: 0.116 AC: 402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.92
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1019156; hg19: chr17-14574644;