6-18480788-C-T

Variant names:

• chr6-18480788-C-T
• rs567621

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 0.934 in 152,286 control chromosomes in the GnomAD database, including 66,490 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 0.93 (66490 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.820
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.945 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: 0.934 AC: 142158 AN: 152168 Hom.: 66434 Cov.: 33

Gnomad AFR AF: 0.902

Gnomad AMI AF: 0.979

Gnomad AMR AF: 0.926

Gnomad ASJ AF: 0.948

Gnomad EAS AF: 0.954

Gnomad SAS AF: 0.903

Gnomad FIN AF: 0.962

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.951

Gnomad OTH AF: 0.931

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

GnomAD4 genome AF: 0.934 AC: 142272 AN: 152286 Hom.: 66490 Cov.: 33 AF XY: 0.934 AC XY: 69545 AN XY: 74452

African (AFR) AF: 0.902 AC: 37485 AN: 41552

American (AMR) AF: 0.926 AC: 14174 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.948 AC: 3291 AN: 3472

East Asian (EAS) AF: 0.954 AC: 4947 AN: 5186

South Asian (SAS) AF: 0.903 AC: 4348 AN: 4814

European-Finnish (FIN) AF: 0.962 AC: 10208 AN: 10616

Middle Eastern (MID) AF: 0.952 AC: 280 AN: 294

European-Non Finnish (NFE) AF: 0.951 AC: 64683 AN: 68026

Other (OTH) AF: 0.930 AC: 1965 AN: 2114

Alfa AF: 0.945 Hom.: 106309

Bravo AF: 0.932

Asia WGS AF: 0.919 AC: 3199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.64
DANN	Benign	0.48
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs567621; hg19: chr6-18481019;