rs17705188

chr19-35290413-A-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 0.0447 in 152,220 control chromosomes in the GnomAD database, including 195 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 0.045 (195 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0708 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: 0.0446 AC: 6789 AN: 152102 Hom.: 193 Cov.: 32

Gnomad AFR AF: 0.0107

Gnomad AMI AF: 0.0747

Gnomad AMR AF: 0.0628

Gnomad ASJ AF: 0.0591

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0772

Gnomad FIN AF: 0.0360

Gnomad MID AF: 0.0605

Gnomad NFE AF: 0.0621

Gnomad OTH AF: 0.0557

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

GnomAD4 genome AF: 0.0447 AC: 6799 AN: 152220 Hom.: 195 Cov.: 32 AF XY: 0.0437 AC XY: 3252 AN XY: 74422

Gnomad4 AFR AF: 0.0107

Gnomad4 AMR AF: 0.0631

Gnomad4 ASJ AF: 0.0591

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0773

Gnomad4 FIN AF: 0.0360

Gnomad4 NFE AF: 0.0621

Gnomad4 OTH AF: 0.0551

Alfa AF: 0.0640 Hom.: 310

Bravo AF: 0.0467

Asia WGS AF: 0.0280 AC: 98 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.3
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17705188; hg19: chr19-35781316;