20-6815572-C-T

Variant names:

• chr20-6815572-C-T
• rs996544

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 0.111 in 152,052 control chromosomes in the GnomAD database, including 1,246 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 0.11 (1246 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.920
• Publications: 6 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 (AFR) allele frequency at 95% confidence interval = 0.202 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: 0.111 AC: 16807 AN: 151934 Hom.: 1243 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.0549

Gnomad AMR AF: 0.0883

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0450

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.0416

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0703

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.111 AC: 16823 AN: 152052 Hom.: 1246 Cov.: 32 AF XY: 0.111 AC XY: 8223 AN XY: 74330

African (AFR) AF: 0.206 AC: 8530 AN: 41462

American (AMR) AF: 0.0880 AC: 1345 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 359 AN: 3466

East Asian (EAS) AF: 0.0451 AC: 232 AN: 5144

South Asian (SAS) AF: 0.168 AC: 805 AN: 4804

European-Finnish (FIN) AF: 0.0416 AC: 441 AN: 10608

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.0703 AC: 4779 AN: 67970

Other (OTH) AF: 0.111 AC: 234 AN: 2110

Alfa AF: 0.0838 Hom.: 1254

Bravo AF: 0.116

Asia WGS AF: 0.138 AC: 478 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	0.43
DANN	Benign	0.44
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs996544; hg19: chr20-6796219;