rs16883019

Variant names:

• chr6-19969407-T-C
• rs16883019

Your query was ambiguous. Multiple possible variants found:

• chr6-19969407-T-C
• chr6-19969407-T-G

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 0.0906 in 152,238 control chromosomes in the GnomAD database, including 892 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 0.091 (892 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.509
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0906 AC: 13780 AN: 152120 Hom.: 892 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0971

Gnomad ASJ AF: 0.0799

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0468

Gnomad OTH AF: 0.0903

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

GnomAD4 genome AF: 0.0906 AC: 13797 AN: 152238 Hom.: 892 Cov.: 32 AF XY: 0.0979 AC XY: 7288 AN XY: 74448

African (AFR) AF: 0.118 AC: 4900 AN: 41540

American (AMR) AF: 0.0971 AC: 1486 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0799 AC: 277 AN: 3466

East Asian (EAS) AF: 0.301 AC: 1552 AN: 5164

South Asian (SAS) AF: 0.201 AC: 969 AN: 4820

European-Finnish (FIN) AF: 0.113 AC: 1199 AN: 10612

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0468 AC: 3186 AN: 68020

Other (OTH) AF: 0.0889 AC: 188 AN: 2114

Alfa AF: 0.0625 Hom.: 1552

Bravo AF: 0.0888

Asia WGS AF: 0.193 AC: 670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.84
DANN	Benign	0.74
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs16883019; hg19: chr6-19969638;