rs17345545

Variant names:

• chr1-4905092-A-C
• rs17345545

Your query was ambiguous. Multiple possible variants found:

• chr1-4905092-A-C
• chr1-4905092-A-T

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 0.202 in 152,134 control chromosomes in the GnomAD database, including 3,456 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 0.20 (3456 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.251 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: 0.202 AC: 30682 AN: 152014 Hom.: 3453 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.202 AC: 30709 AN: 152134 Hom.: 3456 Cov.: 32 AF XY: 0.197 AC XY: 14620 AN XY: 74378

African (AFR) AF: 0.139 AC: 5771 AN: 41508

American (AMR) AF: 0.142 AC: 2174 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 634 AN: 3466

East Asian (EAS) AF: 0.194 AC: 1003 AN: 5166

South Asian (SAS) AF: 0.221 AC: 1065 AN: 4816

European-Finnish (FIN) AF: 0.177 AC: 1874 AN: 10584

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.255 AC: 17303 AN: 67980

Other (OTH) AF: 0.188 AC: 397 AN: 2114

Alfa AF: 0.233 Hom.: 7286

Bravo AF: 0.197

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.24
DANN	Benign	0.74
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs17345545; hg19: chr1-4965152;