20-6781118-T-C

Variant names:

• chr20-6781118-T-C
• rs235770

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 0.706 in 152,104 control chromosomes in the GnomAD database, including 39,152 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 0.71 (39152 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.193
• Publications: 27 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.887 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.706 AC: 107254 AN: 151986 Hom.: 39107 Cov.: 32

Gnomad AFR AF: 0.895

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.821

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.722

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

GnomAD4 genome AF: 0.706 AC: 107346 AN: 152104 Hom.: 39152 Cov.: 32 AF XY: 0.700 AC XY: 51996 AN XY: 74322

African (AFR) AF: 0.895 AC: 37155 AN: 41518

American (AMR) AF: 0.684 AC: 10462 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.821 AC: 2850 AN: 3470

East Asian (EAS) AF: 0.672 AC: 3483 AN: 5180

South Asian (SAS) AF: 0.569 AC: 2742 AN: 4816

European-Finnish (FIN) AF: 0.575 AC: 6054 AN: 10536

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.622 AC: 42300 AN: 67982

Other (OTH) AF: 0.714 AC: 1507 AN: 2110

Alfa AF: 0.662 Hom.: 64134

Bravo AF: 0.727

Asia WGS AF: 0.610 AC: 2119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.2
DANN	Benign	0.64
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs235770; hg19: chr20-6761765;