rs6092477

Variant names:

• chr20-57416639-G-A
• rs6092477

Your query was ambiguous. Multiple possible variants found:

• chr20-57416639-G-A
• chr20-57416639-G-C
• chr20-57416639-G-T

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 0.361 in 152,122 control chromosomes in the GnomAD database, including 10,346 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 0.36 (10346 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.255
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.491 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: 0.361 AC: 54861 AN: 152004 Hom.: 10332 Cov.: 34

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.361 AC: 54920 AN: 152122 Hom.: 10346 Cov.: 34 AF XY: 0.367 AC XY: 27251 AN XY: 74352

African (AFR) AF: 0.363 AC: 15074 AN: 41500

American (AMR) AF: 0.481 AC: 7353 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 900 AN: 3466

East Asian (EAS) AF: 0.507 AC: 2616 AN: 5160

South Asian (SAS) AF: 0.289 AC: 1392 AN: 4824

European-Finnish (FIN) AF: 0.427 AC: 4526 AN: 10592

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21729 AN: 67980

Other (OTH) AF: 0.380 AC: 803 AN: 2112

Alfa AF: 0.339 Hom.: 40886

Bravo AF: 0.372

Asia WGS AF: 0.442 AC: 1537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.55
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs6092477; hg19: chr20-55991695;