17-41036545-A-T

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 0.0708 in 152,182 control chromosomes in the GnomAD database, including 754 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 0.071 (754 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.158 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: 0.0707 AC: 10754 AN: 152064 Hom.: 753 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0242

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.0242

Gnomad FIN AF: 0.0309

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0133

Gnomad OTH AF: 0.0684

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

GnomAD4 genome AF: 0.0708 AC: 10774 AN: 152182 Hom.: 754 Cov.: 32 AF XY: 0.0718 AC XY: 5343 AN XY: 74414

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.0242

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.0228

Gnomad4 FIN AF: 0.0309

Gnomad4 NFE AF: 0.0133

Gnomad4 OTH AF: 0.0691

Alfa AF: 0.0116 Hom.: 11

Bravo AF: 0.0833

Asia WGS AF: 0.117 AC: 405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.15
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4442876; hg19: chr17-39192797;