rs7689003

chr4-45123808-A-G

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 0.666 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.707

Gnomad4 AMR AF: 0.621

Gnomad4 ASJ AF: 0.723

Gnomad4 EAS AF: 0.562

Gnomad4 SAS AF: 0.553

Gnomad4 FIN AF: 0.694

Gnomad4 NFE AF: 0.663

Gnomad4 OTH AF: 0.666

Alfa AF: 0.661 Hom.: 67436

Bravo AF: 0.665

Asia WGS AF: 0.566 AC: 1967 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	3.3
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7689003; hg19: chr4-45125825;