rs9364703

Positions:

• chr6-163829642-A-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 0.412 in 152,150 control chromosomes in the GnomAD database, including 14,830 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 0.41 (14830 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.616 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: 0.412 AC: 62700 AN: 152032 Hom.: 14815 Cov.: 33

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.412 AC: 62729 AN: 152150 Hom.: 14830 Cov.: 33 AF XY: 0.417 AC XY: 31002 AN XY: 74372

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.583

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.634

Gnomad4 SAS AF: 0.536

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.480

Gnomad4 OTH AF: 0.445

Alfa AF: 0.459 Hom.: 2976

Bravo AF: 0.410

Asia WGS AF: 0.554 AC: 1926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.97
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: rs9364703; hg19: chr6-164250674;