chr20-6868719-T-C

Variant names:

• chr20-6868719-T-C
• rs10485706

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 0.0946 in 152,230 control chromosomes in the GnomAD database, including 2,148 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 0.095 (2148 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.144
• Publications: 0 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 = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0941 AC: 14318 AN: 152112 Hom.: 2119 Cov.: 33

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.0220

Gnomad AMR AF: 0.0422

Gnomad ASJ AF: 0.0109

Gnomad EAS AF: 0.0198

Gnomad SAS AF: 0.0166

Gnomad FIN AF: 0.00113

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.00575

Gnomad OTH AF: 0.0781

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

GnomAD4 genome AF: 0.0946 AC: 14395 AN: 152230 Hom.: 2148 Cov.: 33 AF XY: 0.0911 AC XY: 6777 AN XY: 74428

African (AFR) AF: 0.312 AC: 12928 AN: 41502

American (AMR) AF: 0.0421 AC: 645 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0109 AC: 38 AN: 3472

East Asian (EAS) AF: 0.0199 AC: 103 AN: 5184

South Asian (SAS) AF: 0.0168 AC: 81 AN: 4822

European-Finnish (FIN) AF: 0.00113 AC: 12 AN: 10618

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.00575 AC: 391 AN: 68014

Other (OTH) AF: 0.0773 AC: 163 AN: 2110

Alfa AF: 0.0544 Hom.: 147

Bravo AF: 0.109

Asia WGS AF: 0.0460 AC: 161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.5
DANN	Benign	0.58
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs10485706; hg19: chr20-6849366;