rs6140124

Variant names:

• chr20-6933970-T-C
• rs6140124

Your query was ambiguous. Multiple possible variants found:

• chr20-6933970-T-C
• chr20-6933970-T-G

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 0.0546 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0104 AC: 431 AN: 41550

American (AMR) AF: 0.0335 AC: 512 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0660 AC: 229 AN: 3472

East Asian (EAS) AF: 0.459 AC: 2364 AN: 5154

South Asian (SAS) AF: 0.220 AC: 1061 AN: 4820

European-Finnish (FIN) AF: 0.0665 AC: 705 AN: 10602

Middle Eastern (MID) AF: 0.0753 AC: 22 AN: 292

European-Non Finnish (NFE) AF: 0.0418 AC: 2839 AN: 67978

Other (OTH) AF: 0.0662 AC: 140 AN: 2114

Alfa AF: 0.0494 Hom.: 309

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
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs6140124; hg19: chr20-6914617;