rs13447427

Positions:

• chr7-5525803-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 0.0702 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0701 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

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.0332

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.0122

Gnomad4 SAS AF: 0.0399

Gnomad4 FIN AF: 0.0554

Gnomad4 NFE AF: 0.0409

Gnomad4 OTH AF: 0.0625

Alfa AF: 0.0525 Hom.: 205

Bravo AF: 0.0718

Asia WGS AF: 0.0600 AC: 208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13447427; hg19: chr7-5565434;