7-45894560-A-G

Variant names:

• chr7-45894560-A-G
• rs9658239

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 0.104 in 152,176 control chromosomes in the GnomAD database, including 1,005 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 0.10 (1005 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15773 AN: 152058 Hom.: 1007 Cov.: 32

Gnomad AFR AF: 0.0298

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.0813

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.0516

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.104 AC: 15770 AN: 152176 Hom.: 1005 Cov.: 32 AF XY: 0.103 AC XY: 7693 AN XY: 74374

African (AFR) AF: 0.0297 AC: 1235 AN: 41542

American (AMR) AF: 0.0812 AC: 1242 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 744 AN: 3470

East Asian (EAS) AF: 0.192 AC: 992 AN: 5156

South Asian (SAS) AF: 0.0518 AC: 250 AN: 4822

European-Finnish (FIN) AF: 0.164 AC: 1738 AN: 10590

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9260 AN: 67990

Other (OTH) AF: 0.123 AC: 259 AN: 2112

Alfa AF: 0.120 Hom.: 1547

Bravo AF: 0.0959

Asia WGS AF: 0.0980 AC: 338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.6
DANN	Benign	0.54
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs9658239; hg19: chr7-45934159;