rs7689003

Variant names:

• chr4-45123808-A-G
• rs7689003

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 0.666 in 151,978 control chromosomes in the GnomAD database, including 33,839 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 0.67 (33839 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.7 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: 0.666 AC: 101144 AN: 151860 Hom.: 33799 Cov.: 32

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.672

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

GnomAD4 genome AF: 0.666 AC: 101227 AN: 151978 Hom.: 33839 Cov.: 32 AF XY: 0.661 AC XY: 49103 AN XY: 74258

African (AFR) AF: 0.707 AC: 29305 AN: 41468

American (AMR) AF: 0.621 AC: 9452 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.723 AC: 2507 AN: 3468

East Asian (EAS) AF: 0.562 AC: 2892 AN: 5150

South Asian (SAS) AF: 0.553 AC: 2665 AN: 4818

European-Finnish (FIN) AF: 0.694 AC: 7349 AN: 10594

Middle Eastern (MID) AF: 0.671 AC: 196 AN: 292

European-Non Finnish (NFE) AF: 0.663 AC: 45011 AN: 67934

Other (OTH) AF: 0.666 AC: 1405 AN: 2110

Alfa AF: 0.663 Hom.: 106849

Bravo AF: 0.665

Asia WGS AF: 0.566 AC: 1967 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.3
DANN	Benign	0.48
PhyloP100		0.024

Splicing

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

Other links and lift over

dbSNP: rs7689003; hg19: chr4-45125825;