rs17385878

Variant names:

• chr1-160607366-C-T
• rs17385878

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 0.27 in 151,776 control chromosomes in the GnomAD database, including 5,863 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 0.27 (5863 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.312 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: 0.270 AC: 40948 AN: 151658 Hom.: 5864 Cov.: 31

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.270 AC: 40944 AN: 151776 Hom.: 5863 Cov.: 31 AF XY: 0.261 AC XY: 19351 AN XY: 74138

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.303

Alfa AF: 0.277 Hom.: 843

Bravo AF: 0.275

Asia WGS AF: 0.169 AC: 590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.4
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17385878; hg19: chr1-160577156;