rs4846647

Variant names:

• chr1-220451945-G-A
• rs4846647

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 0.694 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.694 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

Gnomad4 AFR AF: 0.513

Gnomad4 AMR AF: 0.711

Gnomad4 ASJ AF: 0.724

Gnomad4 EAS AF: 0.529

Gnomad4 SAS AF: 0.731

Gnomad4 FIN AF: 0.827

Gnomad4 NFE AF: 0.785

Gnomad4 OTH AF: 0.715

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4846647; hg19: chr1-220625287;