17-58281401-C-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 0.239 in 151,690 control chromosomes in the GnomAD database, including 4,673 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as protective,risk factor (no stars).

• Frequency: Genomes: 𝑓 0.24 (4673 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: protective; risk factor no assertion criteria provided B:1 O:1
• Conservation: PhyloP100: 0.305

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.329 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: 0.239 AC: 36187 AN: 151572 Hom.: 4664 Cov.: 31

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.239 AC: 36233 AN: 151690 Hom.: 4673 Cov.: 31 AF XY: 0.237 AC XY: 17564 AN XY: 74104

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.255

Alfa AF: 0.0876 Hom.: 105

Bravo AF: 0.247

Asia WGS AF: 0.127 AC: 447 AN: 3476

ClinVar

Significance: protective; risk factor

Submissions summary: Benign:1 Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Lung cancer, protection against, in smokers Benign:1

protective, no assertion criteria provided

literature only

OMIM

Feb 01, 2007

- -

Alzheimer disease, susceptibility to Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Feb 01, 2007

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	8.3
Dann	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2333227; hg19: chr17-56358762;