rs6117432

Variant names:

• chr20-6783889-C-T
• rs6117432

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 0.258 in 152,020 control chromosomes in the GnomAD database, including 5,319 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 0.26 (5319 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260
• Publications: 5 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 (EAS) allele frequency at 95% confidence interval = 0.447 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: 0.258 AC: 39251 AN: 151902 Hom.: 5305 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.258 AC: 39285 AN: 152020 Hom.: 5319 Cov.: 32 AF XY: 0.265 AC XY: 19696 AN XY: 74292

African (AFR) AF: 0.240 AC: 9947 AN: 41446

American (AMR) AF: 0.276 AC: 4211 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1080 AN: 3464

East Asian (EAS) AF: 0.462 AC: 2377 AN: 5144

South Asian (SAS) AF: 0.294 AC: 1411 AN: 4802

European-Finnish (FIN) AF: 0.311 AC: 3289 AN: 10578

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.236 AC: 16035 AN: 67994

Other (OTH) AF: 0.285 AC: 601 AN: 2112

Alfa AF: 0.242 Hom.: 7519

Bravo AF: 0.253

Asia WGS AF: 0.357 AC: 1242 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	0.87
DANN	Benign	0.75
PhyloP100		-0.026

Splicing

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

Other links and lift over

dbSNP: rs6117432; hg19: chr20-6764536;