17-58281401-C-T

Variant names:

• chr17-58281401-C-T
• rs2333227

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 288 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.333 AC: 13764 AN: 41308

American (AMR) AF: 0.212 AC: 3235 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 820 AN: 3464

East Asian (EAS) AF: 0.122 AC: 627 AN: 5138

South Asian (SAS) AF: 0.141 AC: 679 AN: 4800

European-Finnish (FIN) AF: 0.201 AC: 2114 AN: 10528

Middle Eastern (MID) AF: 0.243 AC: 71 AN: 292

European-Non Finnish (NFE) AF: 0.209 AC: 14202 AN: 67874

Other (OTH) AF: 0.255 AC: 539 AN: 2112

Alfa AF: 0.102 Hom.: 146

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

Feb 01, 2007

OMIM

Significance: protective

Review Status: no assertion criteria provided

Collection Method: literature only

ALZHEIMER DISEASE, SUSCEPTIBILITY TO Other:1

Feb 01, 2007

OMIM

Significance: risk factor

Review Status: no assertion criteria provided

Collection Method: literature only

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.3
DANN	Benign	0.21
PhyloP100		0.30
PromoterAI		-0.0062	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2333227; hg19: chr17-56358762;