8-20494400-T-C

Variant names:

• chr8-20494400-T-C
• rs11204117

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 0.267 in 152,102 control chromosomes in the GnomAD database, including 8,822 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 0.27 (8822 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.608
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.59 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40525 AN: 151984 Hom.: 8791 Cov.: 32

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.0469

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.267 AC: 40626 AN: 152102 Hom.: 8822 Cov.: 32 AF XY: 0.261 AC XY: 19387 AN XY: 74384

African (AFR) AF: 0.596 AC: 24703 AN: 41434

American (AMR) AF: 0.270 AC: 4121 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 598 AN: 3468

East Asian (EAS) AF: 0.195 AC: 1006 AN: 5168

South Asian (SAS) AF: 0.215 AC: 1034 AN: 4812

European-Finnish (FIN) AF: 0.0469 AC: 498 AN: 10622

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7982 AN: 68000

Other (OTH) AF: 0.237 AC: 501 AN: 2110

Alfa AF: 0.166 Hom.: 13699

Bravo AF: 0.301

Asia WGS AF: 0.253 AC: 880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	15
DANN	Benign	0.59
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs11204117; hg19: chr8-20351911;