rs9365619

Variant names:

• chr6-163830714-A-C
• rs9365619

Your query was ambiguous. Multiple possible variants found:

• chr6-163830714-A-C
• chr6-163830714-A-G
• chr6-163830714-A-T

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 0.512 in 151,808 control chromosomes in the GnomAD database, including 20,619 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 0.51 (20619 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.486

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.639 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: 0.511 AC: 77587 AN: 151690 Hom.: 20595 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.512 AC: 77651 AN: 151808 Hom.: 20619 Cov.: 32 AF XY: 0.513 AC XY: 38048 AN XY: 74168

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.650

Gnomad4 ASJ AF: 0.617

Gnomad4 EAS AF: 0.635

Gnomad4 SAS AF: 0.606

Gnomad4 FIN AF: 0.484

Gnomad4 NFE AF: 0.538

Gnomad4 OTH AF: 0.547

Alfa AF: 0.530 Hom.: 2742

Bravo AF: 0.519

Asia WGS AF: 0.605 AC: 2105 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	0.11
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9365619; hg19: chr6-164251746;