rs6140124

chr20-6933970-T-Cchr20-6933970-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0546 in 152,170 control chromosomes in the GnomAD database, including 811 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 0.055 (811 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.789

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0547 AC: 8317 AN: 152054 Hom.: 816 Cov.: 33

Gnomad AFR AF: 0.0104

Gnomad AMI AF: 0.00989

Gnomad AMR AF: 0.0336

Gnomad ASJ AF: 0.0660

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.0665

Gnomad MID AF: 0.0732

Gnomad NFE AF: 0.0418

Gnomad OTH AF: 0.0621

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

GnomAD4 genome AF: 0.0546 AC: 8312 AN: 152170 Hom.: 811 Cov.: 33 AF XY: 0.0603 AC XY: 4484 AN XY: 74392

Gnomad4 AFR AF: 0.0104

Gnomad4 AMR AF: 0.0335

Gnomad4 ASJ AF: 0.0660

Gnomad4 EAS AF: 0.459

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.0665

Gnomad4 NFE AF: 0.0418

Gnomad4 OTH AF: 0.0662

Alfa AF: 0.0503 Hom.: 216

Bravo AF: 0.0491

Asia WGS AF: 0.301 AC: 1045 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.1
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6140124; hg19: chr20-6914617;