rs1979605

Variant names:

• chr4-55552706-A-G
• rs1979605

Your query was ambiguous. Multiple possible variants found:

• chr4-55552706-A-G
• chr4-55552706-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 0.75 in 152,090 control chromosomes in the GnomAD database, including 43,056 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 0.75 (43056 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.381
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.879 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: 0.750 AC: 113967 AN: 151972 Hom.: 43022 Cov.: 31

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.751

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

GnomAD4 genome AF: 0.750 AC: 114053 AN: 152090 Hom.: 43056 Cov.: 31 AF XY: 0.745 AC XY: 55388 AN XY: 74334

African (AFR) AF: 0.815 AC: 33810 AN: 41468

American (AMR) AF: 0.765 AC: 11709 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.763 AC: 2646 AN: 3466

East Asian (EAS) AF: 0.901 AC: 4653 AN: 5164

South Asian (SAS) AF: 0.627 AC: 3027 AN: 4824

European-Finnish (FIN) AF: 0.643 AC: 6792 AN: 10562

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.720 AC: 48941 AN: 67990

Other (OTH) AF: 0.753 AC: 1590 AN: 2112

Alfa AF: 0.724 Hom.: 9098

Bravo AF: 0.770

Asia WGS AF: 0.738 AC: 2567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.3
DANN	Benign	0.56
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs1979605; hg19: chr4-56418873;