20-6961773-T-C

Variant names:

• chr20-6961773-T-C
• rs6054631

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 0.289 in 152,158 control chromosomes in the GnomAD database, including 7,168 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 0.29 (7168 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.439 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: 0.288 AC: 43808 AN: 152040 Hom.: 7138 Cov.: 33

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.289 AC: 43904 AN: 152158 Hom.: 7168 Cov.: 33 AF XY: 0.286 AC XY: 21255 AN XY: 74390

African (AFR) AF: 0.444 AC: 18435 AN: 41510

American (AMR) AF: 0.185 AC: 2829 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 594 AN: 3472

East Asian (EAS) AF: 0.176 AC: 909 AN: 5174

South Asian (SAS) AF: 0.283 AC: 1367 AN: 4824

European-Finnish (FIN) AF: 0.237 AC: 2508 AN: 10594

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.240 AC: 16334 AN: 67990

Other (OTH) AF: 0.259 AC: 547 AN: 2112

Alfa AF: 0.251 Hom.: 21701

Bravo AF: 0.290

Asia WGS AF: 0.286 AC: 999 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.5
DANN	Benign	0.58
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs6054631; hg19: chr20-6942420;