7-45564030-A-G

Variant names:

• chr7-45564030-A-G
• rs1007572

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 0.282 in 152,004 control chromosomes in the GnomAD database, including 7,636 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 0.28 (7636 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.183
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.491 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: 0.282 AC: 42836 AN: 151884 Hom.: 7613 Cov.: 32

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.282 AC: 42912 AN: 152004 Hom.: 7636 Cov.: 32 AF XY: 0.284 AC XY: 21066 AN XY: 74290

African (AFR) AF: 0.481 AC: 19914 AN: 41422

American (AMR) AF: 0.285 AC: 4351 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 772 AN: 3466

East Asian (EAS) AF: 0.508 AC: 2608 AN: 5138

South Asian (SAS) AF: 0.322 AC: 1550 AN: 4818

European-Finnish (FIN) AF: 0.150 AC: 1589 AN: 10594

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11456 AN: 67976

Other (OTH) AF: 0.246 AC: 520 AN: 2114

Alfa AF: 0.189 Hom.: 3590

Bravo AF: 0.298

Asia WGS AF: 0.426 AC: 1478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	8.0
DANN	Benign	0.79
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs1007572; hg19: chr7-45603629;