chr6-47349576-C-T

Variant names:

• chr6-47349576-C-T
• rs6918220

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 0.102 in 152,142 control chromosomes in the GnomAD database, including 1,876 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 0.10 (1876 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.529
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15524 AN: 152024 Hom.: 1863 Cov.: 32

Gnomad AFR AF: 0.0957

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.0605

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.0550

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0453

Gnomad OTH AF: 0.0970

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

GnomAD4 genome AF: 0.102 AC: 15573 AN: 152142 Hom.: 1876 Cov.: 32 AF XY: 0.109 AC XY: 8093 AN XY: 74388

African (AFR) AF: 0.0961 AC: 3987 AN: 41506

American (AMR) AF: 0.240 AC: 3675 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0605 AC: 210 AN: 3470

East Asian (EAS) AF: 0.600 AC: 3097 AN: 5160

South Asian (SAS) AF: 0.148 AC: 711 AN: 4812

European-Finnish (FIN) AF: 0.0550 AC: 583 AN: 10596

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0453 AC: 3081 AN: 67996

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

Alfa AF: 0.0738 Hom.: 2419

Bravo AF: 0.121

Asia WGS AF: 0.342 AC: 1186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.7
DANN	Benign	0.44
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs6918220; hg19: chr6-47317312;