chr6-100363657-C-T

Variant names:

• chr6-100363657-C-T
• rs17792983

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 0.238 in 152,066 control chromosomes in the GnomAD database, including 4,841 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 0.24 (4841 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.954
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.309 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: 0.238 AC: 36194 AN: 151948 Hom.: 4827 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.238 AC: 36203 AN: 152066 Hom.: 4841 Cov.: 32 AF XY: 0.233 AC XY: 17354 AN XY: 74340

African (AFR) AF: 0.120 AC: 4967 AN: 41506

American (AMR) AF: 0.239 AC: 3642 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1088 AN: 3472

East Asian (EAS) AF: 0.185 AC: 957 AN: 5166

South Asian (SAS) AF: 0.165 AC: 798 AN: 4826

European-Finnish (FIN) AF: 0.246 AC: 2604 AN: 10564

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.312 AC: 21210 AN: 67972

Other (OTH) AF: 0.275 AC: 578 AN: 2104

Alfa AF: 0.281 Hom.: 9429

Bravo AF: 0.233

Asia WGS AF: 0.210 AC: 726 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.3
DANN	Benign	0.69
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs17792983; hg19: chr6-100811533;