rs1860190

Positions:

• chr17-34249554-T-A
• chr17-34249554-T-G

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 0.473 in 152,160 control chromosomes in the GnomAD database, including 18,427 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 0.47 (18427 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71914 AN: 152042 Hom.: 18386 Cov.: 33

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.473 AC: 72008 AN: 152160 Hom.: 18427 Cov.: 33 AF XY: 0.476 AC XY: 35444 AN XY: 74386

Gnomad4 AFR AF: 0.666

Gnomad4 AMR AF: 0.542

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.559

Gnomad4 SAS AF: 0.446

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.454

Alfa AF: 0.413 Hom.: 1732

Bravo AF: 0.492

Asia WGS AF: 0.506 AC: 1758 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1860190; hg19: chr17-32576573;