6-15779015-A-G

Variant names:

• chr6-15779015-A-G
• rs220913

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 0.519 in 152,046 control chromosomes in the GnomAD database, including 20,999 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 0.52 (20999 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.579 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: 0.519 AC: 78889 AN: 151928 Hom.: 20978 Cov.: 33

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.519 AC: 78953 AN: 152046 Hom.: 20999 Cov.: 33 AF XY: 0.516 AC XY: 38368 AN XY: 74318

African (AFR) AF: 0.428 AC: 17734 AN: 41448

American (AMR) AF: 0.516 AC: 7880 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2086 AN: 3472

East Asian (EAS) AF: 0.276 AC: 1423 AN: 5164

South Asian (SAS) AF: 0.447 AC: 2158 AN: 4826

European-Finnish (FIN) AF: 0.590 AC: 6237 AN: 10580

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.584 AC: 39711 AN: 67962

Other (OTH) AF: 0.519 AC: 1097 AN: 2112

Alfa AF: 0.541 Hom.: 2718

Bravo AF: 0.508

Asia WGS AF: 0.360 AC: 1252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.28
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs220913; hg19: chr6-15779246;