rs9364703

Variant names:

• chr6-163829642-A-G
• rs9364703

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 0.412 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.178 AC: 7388 AN: 41544

American (AMR) AF: 0.583 AC: 8905 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1502 AN: 3472

East Asian (EAS) AF: 0.634 AC: 3277 AN: 5170

South Asian (SAS) AF: 0.536 AC: 2584 AN: 4822

European-Finnish (FIN) AF: 0.463 AC: 4892 AN: 10562

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.480 AC: 32656 AN: 67976

Other (OTH) AF: 0.445 AC: 939 AN: 2112

Alfa AF: 0.452 Hom.: 3001

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
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs9364703; hg19: chr6-164250674;