rs1568645

Variant names:

• chr7-40111556-G-A
• rs1568645

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 0.498 in 151,926 control chromosomes in the GnomAD database, including 19,604 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 0.50 (19604 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75587 AN: 151810 Hom.: 19574 Cov.: 32

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.498 AC: 75672 AN: 151926 Hom.: 19604 Cov.: 32 AF XY: 0.499 AC XY: 37036 AN XY: 74260

African (AFR) AF: 0.637 AC: 26389 AN: 41420

American (AMR) AF: 0.446 AC: 6811 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1931 AN: 3470

East Asian (EAS) AF: 0.341 AC: 1759 AN: 5154

South Asian (SAS) AF: 0.545 AC: 2625 AN: 4814

European-Finnish (FIN) AF: 0.462 AC: 4867 AN: 10524

Middle Eastern (MID) AF: 0.623 AC: 182 AN: 292

European-Non Finnish (NFE) AF: 0.438 AC: 29741 AN: 67970

Other (OTH) AF: 0.513 AC: 1084 AN: 2114

Alfa AF: 0.488 Hom.: 2438

Bravo AF: 0.503

Asia WGS AF: 0.469 AC: 1629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.7
DANN	Benign	0.36
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs1568645; hg19: chr7-40151155;