rs4846647

Variant names:

• chr1-220451945-G-A
• rs4846647

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 0.694 in 152,100 control chromosomes in the GnomAD database, including 37,874 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 0.69 (37874 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.670
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.694 AC: 105484 AN: 151980 Hom.: 37876 Cov.: 33

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.529

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.704

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.694 AC: 105512 AN: 152100 Hom.: 37874 Cov.: 33 AF XY: 0.696 AC XY: 51713 AN XY: 74352

African (AFR) AF: 0.513 AC: 21271 AN: 41472

American (AMR) AF: 0.711 AC: 10855 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 2511 AN: 3468

East Asian (EAS) AF: 0.529 AC: 2739 AN: 5178

South Asian (SAS) AF: 0.731 AC: 3525 AN: 4822

European-Finnish (FIN) AF: 0.827 AC: 8749 AN: 10580

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.785 AC: 53370 AN: 67986

Other (OTH) AF: 0.715 AC: 1510 AN: 2112

Alfa AF: 0.742 Hom.: 8544

Bravo AF: 0.672

Asia WGS AF: 0.615 AC: 2140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.1
DANN	Benign	0.23
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs4846647; hg19: chr1-220625287;