rs9359049

Positions:

• chr6-73992213-T-A
• chr6-73992213-T-C

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 0.0868 in 152,242 control chromosomes in the GnomAD database, including 730 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 0.087 (730 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.601

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0868 AC: 13198 AN: 152122 Hom.: 728 Cov.: 32

Gnomad AFR AF: 0.0693

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.0466

Gnomad FIN AF: 0.0676

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0718

Gnomad OTH AF: 0.0994

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

GnomAD4 genome AF: 0.0868 AC: 13216 AN: 152242 Hom.: 730 Cov.: 32 AF XY: 0.0883 AC XY: 6573 AN XY: 74444

Gnomad4 AFR AF: 0.0693

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.0469

Gnomad4 FIN AF: 0.0676

Gnomad4 NFE AF: 0.0718

Gnomad4 OTH AF: 0.0993

Alfa AF: 0.0228 Hom.: 6

Bravo AF: 0.0978

Asia WGS AF: 0.144 AC: 500 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.9
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9359049; hg19: chr6-74701929;