rs9380516

Variant names:

• chr6-35534425-T-C
• rs9380516

Your query was ambiguous. Multiple possible variants found:

• chr6-35534425-T-C
• chr6-35534425-T-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 0.849 in 151,958 control chromosomes in the GnomAD database, including 54,794 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 0.85 (54794 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.297

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.87 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: 0.849 AC: 128853 AN: 151840 Hom.: 54743 Cov.: 30

Gnomad AFR AF: 0.877

Gnomad AMI AF: 0.928

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.762

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.841

Gnomad OTH AF: 0.827

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

GnomAD4 genome AF: 0.849 AC: 128968 AN: 151958 Hom.: 54794 Cov.: 30 AF XY: 0.847 AC XY: 62898 AN XY: 74270

Gnomad4 AFR AF: 0.877

Gnomad4 AMR AF: 0.868

Gnomad4 ASJ AF: 0.800

Gnomad4 EAS AF: 0.846

Gnomad4 SAS AF: 0.763

Gnomad4 FIN AF: 0.817

Gnomad4 NFE AF: 0.841

Gnomad4 OTH AF: 0.827

Alfa AF: 0.839 Hom.: 25603

Bravo AF: 0.856

Asia WGS AF: 0.819 AC: 2848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.3
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9380516; hg19: chr6-35502202;