rs13227829

Variant names:

• chr7-9065398-A-G
• rs13227829

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 0.123 in 152,142 control chromosomes in the GnomAD database, including 1,329 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 0.12 (1329 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.824

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.165 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: 0.123 AC: 18695 AN: 152024 Hom.: 1329 Cov.: 32

Gnomad AFR AF: 0.0461

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.0869

Gnomad SAS AF: 0.0703

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.123 AC: 18696 AN: 152142 Hom.: 1329 Cov.: 32 AF XY: 0.120 AC XY: 8910 AN XY: 74372

Gnomad4 AFR AF: 0.0462

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.0862

Gnomad4 SAS AF: 0.0705

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.139

Alfa AF: 0.161 Hom.: 4079

Bravo AF: 0.120

Asia WGS AF: 0.0980 AC: 342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.8
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13227829; hg19: chr7-9105028;