rs4946578

Variant names:

• chr6-121573915-A-G
• rs4946578

Your query was ambiguous. Multiple possible variants found:

• chr6-121573915-A-G
• chr6-121573915-A-T

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 0.542 in 151,898 control chromosomes in the GnomAD database, including 23,020 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 0.54 (23020 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.542 AC: 82303 AN: 151780 Hom.: 22996 Cov.: 31

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.542 AC: 82372 AN: 151898 Hom.: 23020 Cov.: 31 AF XY: 0.551 AC XY: 40870 AN XY: 74214

African (AFR) AF: 0.423 AC: 17507 AN: 41390

American (AMR) AF: 0.660 AC: 10091 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1880 AN: 3468

East Asian (EAS) AF: 0.595 AC: 3062 AN: 5146

South Asian (SAS) AF: 0.546 AC: 2628 AN: 4812

European-Finnish (FIN) AF: 0.681 AC: 7176 AN: 10544

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.562 AC: 38219 AN: 67946

Other (OTH) AF: 0.540 AC: 1139 AN: 2108

Alfa AF: 0.557 Hom.: 108110

Bravo AF: 0.538

Asia WGS AF: 0.568 AC: 1972 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.7
DANN	Benign	0.74
PhyloP100		-0.0020

Splicing

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

Other links and lift over

dbSNP: rs4946578; hg19: chr6-121895061;