rs9359049

Variant names:

• chr6-73992213-T-A
• rs9359049

Your query was ambiguous. Multiple possible variants found:

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

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 0.0868 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
• Publications: 4 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0693 AC: 2878 AN: 41554

American (AMR) AF: 0.153 AC: 2342 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 389 AN: 3468

East Asian (EAS) AF: 0.280 AC: 1448 AN: 5176

South Asian (SAS) AF: 0.0469 AC: 226 AN: 4822

European-Finnish (FIN) AF: 0.0676 AC: 718 AN: 10616

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0718 AC: 4879 AN: 67998

Other (OTH) AF: 0.0993 AC: 210 AN: 2114

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
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs9359049; hg19: chr6-74701929;