rs685001

Positions:

• chr1-47559391-C-A
• chr1-47559391-C-G

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 0.566 in 151,920 control chromosomes in the GnomAD database, including 25,806 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 0.57 (25806 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.566 AC: 85906 AN: 151802 Hom.: 25749 Cov.: 31

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.566 AC: 86023 AN: 151920 Hom.: 25806 Cov.: 31 AF XY: 0.572 AC XY: 42417 AN XY: 74220

Gnomad4 AFR AF: 0.714

Gnomad4 AMR AF: 0.590

Gnomad4 ASJ AF: 0.430

Gnomad4 EAS AF: 0.959

Gnomad4 SAS AF: 0.641

Gnomad4 FIN AF: 0.520

Gnomad4 NFE AF: 0.451

Gnomad4 OTH AF: 0.531

Alfa AF: 0.504 Hom.: 7876

Bravo AF: 0.578

Asia WGS AF: 0.788 AC: 2738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.011
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs685001; hg19: chr1-48025063;