rs6550392

Variant names:

• chr3-36094217-A-C
• rs6550392

Your query was ambiguous. Multiple possible variants found:

• chr3-36094217-A-C
• chr3-36094217-A-G
• chr3-36094217-A-T

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 0.903 in 152,034 control chromosomes in the GnomAD database, including 63,657 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 0.90 (63657 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.511
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.992 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: 0.904 AC: 137268 AN: 151916 Hom.: 63616 Cov.: 32

Gnomad AFR AF: 0.668

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.959

Gnomad ASJ AF: 0.998

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.995

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.998

Gnomad OTH AF: 0.919

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

GnomAD4 genome AF: 0.903 AC: 137362 AN: 152034 Hom.: 63657 Cov.: 32 AF XY: 0.907 AC XY: 67401 AN XY: 74296

African (AFR) AF: 0.669 AC: 27701 AN: 41418

American (AMR) AF: 0.959 AC: 14616 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.998 AC: 3466 AN: 3472

East Asian (EAS) AF: 0.997 AC: 5145 AN: 5158

South Asian (SAS) AF: 0.995 AC: 4786 AN: 4808

European-Finnish (FIN) AF: 1.00 AC: 10627 AN: 10628

Middle Eastern (MID) AF: 0.980 AC: 288 AN: 294

European-Non Finnish (NFE) AF: 0.998 AC: 67880 AN: 67996

Other (OTH) AF: 0.920 AC: 1941 AN: 2110

Alfa AF: 0.938 Hom.: 9649

Bravo AF: 0.889

Asia WGS AF: 0.973 AC: 3382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.8
DANN	Benign	0.77
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs6550392; hg19: chr3-36135709;