rs7335200

chr13-23083379-G-A

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 0.135 in 152,102 control chromosomes in the GnomAD database, including 1,442 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 0.14 (1442 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.158 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: 0.135 AC: 20540 AN: 151984 Hom.: 1432 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.0892

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.135 AC: 20573 AN: 152102 Hom.: 1442 Cov.: 32 AF XY: 0.139 AC XY: 10319 AN XY: 74362

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.0896

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.132

Alfa AF: 0.121 Hom.: 1518

Bravo AF: 0.132

Asia WGS AF: 0.114 AC: 399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.65
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7335200; hg19: chr13-23657518;