rs13232606

Positions:

• chr7-45931511-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 0.033 in 151,884 control chromosomes in the GnomAD database, including 109 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 0.033 (109 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.237

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0331 AC: 5019 AN: 151766 Hom.: 109 Cov.: 32

Gnomad AFR AF: 0.00894

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0220

Gnomad ASJ AF: 0.0537

Gnomad EAS AF: 0.00211

Gnomad SAS AF: 0.0791

Gnomad FIN AF: 0.0292

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0491

Gnomad OTH AF: 0.0326

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

GnomAD4 genome AF: 0.0330 AC: 5014 AN: 151884 Hom.: 109 Cov.: 32 AF XY: 0.0324 AC XY: 2408 AN XY: 74242

Gnomad4 AFR AF: 0.00891

Gnomad4 AMR AF: 0.0219

Gnomad4 ASJ AF: 0.0537

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.0788

Gnomad4 FIN AF: 0.0292

Gnomad4 NFE AF: 0.0491

Gnomad4 OTH AF: 0.0323

Alfa AF: 0.0471 Hom.: 83

Bravo AF: 0.0303

Asia WGS AF: 0.0390 AC: 133 AN: 3424

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.6
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13232606; hg19: chr7-45971110;