rs17361286

Variant names:

• chr1-178552781-C-G
• rs17361286

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 0.29 in 152,164 control chromosomes in the GnomAD database, including 7,600 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 0.29 (7600 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.412 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: 0.291 AC: 44223 AN: 152046 Hom.: 7605 Cov.: 33

Gnomad AFR AF: 0.0972

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.290 AC: 44198 AN: 152164 Hom.: 7600 Cov.: 33 AF XY: 0.289 AC XY: 21522 AN XY: 74376

African (AFR) AF: 0.0969 AC: 4022 AN: 41528

American (AMR) AF: 0.279 AC: 4266 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1214 AN: 3470

East Asian (EAS) AF: 0.427 AC: 2210 AN: 5172

South Asian (SAS) AF: 0.361 AC: 1743 AN: 4822

European-Finnish (FIN) AF: 0.355 AC: 3758 AN: 10576

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.384 AC: 26090 AN: 67982

Other (OTH) AF: 0.279 AC: 589 AN: 2114

Alfa AF: 0.330 Hom.: 1342

Bravo AF: 0.274

Asia WGS AF: 0.354 AC: 1230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.098
DANN	Benign	0.62
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs17361286; hg19: chr1-178521916;