rs7673099

Variant names:

• chr4-60321566-A-C
• rs7673099

Your query was ambiguous. Multiple possible variants found:

• chr4-60321566-A-C
• chr4-60321566-A-G
• chr4-60321566-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 0.696 in 152,026 control chromosomes in the GnomAD database, including 38,933 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 0.70 (38933 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.121
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.82 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: 0.697 AC: 105832 AN: 151908 Hom.: 38936 Cov.: 33

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.794

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.696 AC: 105849 AN: 152026 Hom.: 38933 Cov.: 33 AF XY: 0.693 AC XY: 51521 AN XY: 74320

African (AFR) AF: 0.455 AC: 18864 AN: 41464

American (AMR) AF: 0.765 AC: 11671 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.787 AC: 2732 AN: 3472

East Asian (EAS) AF: 0.526 AC: 2708 AN: 5148

South Asian (SAS) AF: 0.600 AC: 2892 AN: 4824

European-Finnish (FIN) AF: 0.794 AC: 8407 AN: 10588

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.825 AC: 56096 AN: 67962

Other (OTH) AF: 0.716 AC: 1513 AN: 2114

Alfa AF: 0.790 Hom.: 78599

Bravo AF: 0.687

Asia WGS AF: 0.515 AC: 1794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.3
DANN	Benign	0.45
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs7673099; hg19: chr4-61187284;