rs221639

chr6-105084968-C-Achr6-105084968-C-Gchr6-105084968-C-T

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 0.865 in 136,008 control chromosomes in the GnomAD database, including 51,513 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 0.86 (51513 hom., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.835

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 = 0.95 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.865 AC: 117643 AN: 135994 Hom.: 51521 Cov.: 22

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.983

Gnomad AMR AF: 0.911

Gnomad ASJ AF: 0.916

Gnomad EAS AF: 0.973

Gnomad SAS AF: 0.908

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.831

Gnomad NFE AF: 0.928

Gnomad OTH AF: 0.877

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

GnomAD4 genome AF: 0.865 AC: 117640 AN: 136008 Hom.: 51513 Cov.: 22 AF XY: 0.864 AC XY: 55756 AN XY: 64508

Gnomad4 AFR AF: 0.699

Gnomad4 AMR AF: 0.911

Gnomad4 ASJ AF: 0.916

Gnomad4 EAS AF: 0.973

Gnomad4 SAS AF: 0.908

Gnomad4 FIN AF: 0.868

Gnomad4 NFE AF: 0.928

Gnomad4 OTH AF: 0.878

Alfa AF: 0.877 Hom.: 8845

Bravo AF: 0.854

Asia WGS AF: 0.904 AC: 2980 AN: 3294

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.54
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs221639; hg19: chr6-105532843;