chr6-105084968-C-A

Variant names:

• chr6-105084968-C-A
• rs221639

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 0.865 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
• Publications: 1 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 = 0.95 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: 0.865 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

African (AFR) AF: 0.699 AC: 24436 AN: 34948

American (AMR) AF: 0.911 AC: 12033 AN: 13202

Ashkenazi Jewish (ASJ) AF: 0.916 AC: 3102 AN: 3388

East Asian (EAS) AF: 0.973 AC: 4591 AN: 4716

South Asian (SAS) AF: 0.908 AC: 4026 AN: 4436

European-Finnish (FIN) AF: 0.868 AC: 5320 AN: 6126

Middle Eastern (MID) AF: 0.837 AC: 221 AN: 264

European-Non Finnish (NFE) AF: 0.928 AC: 61382 AN: 66154

Other (OTH) AF: 0.878 AC: 1652 AN: 1882

Alfa AF: 0.899 Hom.: 30702

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
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs221639; hg19: chr6-105532843;