rs7335046

Variant names:

• chr13-99389484-G-C
• rs7335046

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 0.798 in 152,142 control chromosomes in the GnomAD database, including 49,049 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 0.80 (49049 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.716
• Publications: 38 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.866 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: 0.798 AC: 121317 AN: 152024 Hom.: 49030 Cov.: 32

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.933

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.893

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.864

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.872

Gnomad OTH AF: 0.809

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

GnomAD4 genome AF: 0.798 AC: 121381 AN: 152142 Hom.: 49049 Cov.: 32 AF XY: 0.796 AC XY: 59229 AN XY: 74374

African (AFR) AF: 0.679 AC: 28136 AN: 41458

American (AMR) AF: 0.765 AC: 11700 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.893 AC: 3096 AN: 3468

East Asian (EAS) AF: 0.672 AC: 3478 AN: 5174

South Asian (SAS) AF: 0.765 AC: 3690 AN: 4824

European-Finnish (FIN) AF: 0.864 AC: 9161 AN: 10608

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.872 AC: 59303 AN: 68000

Other (OTH) AF: 0.806 AC: 1703 AN: 2114

Alfa AF: 0.854 Hom.: 30847

Bravo AF: 0.786

Asia WGS AF: 0.688 AC: 2395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.7
DANN	Benign	0.81
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs7335046; hg19: chr13-100041738;