rs17363368

Variant names:

• chr1-163389043-A-G
• rs17363368

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 0.0493 in 152,144 control chromosomes in the GnomAD database, including 251 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 0.049 (251 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.682
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0689 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: 0.0494 AC: 7508 AN: 152026 Hom.: 251 Cov.: 32

Gnomad AFR AF: 0.0117

Gnomad AMI AF: 0.0286

Gnomad AMR AF: 0.0489

Gnomad ASJ AF: 0.0476

Gnomad EAS AF: 0.0348

Gnomad SAS AF: 0.0329

Gnomad FIN AF: 0.0812

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0706

Gnomad OTH AF: 0.0373

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

GnomAD4 genome AF: 0.0493 AC: 7505 AN: 152144 Hom.: 251 Cov.: 32 AF XY: 0.0486 AC XY: 3615 AN XY: 74384

African (AFR) AF: 0.0116 AC: 483 AN: 41506

American (AMR) AF: 0.0488 AC: 746 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0476 AC: 165 AN: 3470

East Asian (EAS) AF: 0.0348 AC: 180 AN: 5166

South Asian (SAS) AF: 0.0328 AC: 158 AN: 4822

European-Finnish (FIN) AF: 0.0812 AC: 860 AN: 10588

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0705 AC: 4796 AN: 67992

Other (OTH) AF: 0.0369 AC: 78 AN: 2114

Alfa AF: 0.0556 Hom.: 37

Bravo AF: 0.0457

Asia WGS AF: 0.0350 AC: 122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.56
DANN	Benign	0.74
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs17363368; hg19: chr1-163358833;