6-18480788-C-T

Variant names:

• chr6-18480788-C-T
• rs567621

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 0.934 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.934 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

Gnomad4 AFR AF: 0.902

Gnomad4 AMR AF: 0.926

Gnomad4 ASJ AF: 0.948

Gnomad4 EAS AF: 0.954

Gnomad4 SAS AF: 0.903

Gnomad4 FIN AF: 0.962

Gnomad4 NFE AF: 0.951

Gnomad4 OTH AF: 0.930

Alfa AF: 0.947 Hom.: 82736

Bravo AF: 0.932

Asia WGS AF: 0.919 AC: 3199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs567621; hg19: chr6-18481019;