rs13447427

Variant names:

• chr7-5525803-A-G
• rs13447427

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 0.0702 in 152,188 control chromosomes in the GnomAD database, including 528 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 0.070 (528 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.14 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: 0.0701 AC: 10660 AN: 152070 Hom.: 525 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0333

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.0121

Gnomad SAS AF: 0.0396

Gnomad FIN AF: 0.0554

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0409

Gnomad OTH AF: 0.0569

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

GnomAD4 genome AF: 0.0702 AC: 10680 AN: 152188 Hom.: 528 Cov.: 32 AF XY: 0.0692 AC XY: 5147 AN XY: 74412

African (AFR) AF: 0.144 AC: 5956 AN: 41494

American (AMR) AF: 0.0332 AC: 508 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 385 AN: 3470

East Asian (EAS) AF: 0.0122 AC: 63 AN: 5178

South Asian (SAS) AF: 0.0399 AC: 192 AN: 4818

European-Finnish (FIN) AF: 0.0554 AC: 588 AN: 10620

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0409 AC: 2780 AN: 68008

Other (OTH) AF: 0.0625 AC: 132 AN: 2112

Alfa AF: 0.0535 Hom.: 712

Bravo AF: 0.0718

Asia WGS AF: 0.0600 AC: 208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.86
DANN	Benign	0.56
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs13447427; hg19: chr7-5565434;