6-130508549-C-G

Variant names:

• chr6-130508549-C-G
• rs6569686

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 0.529 in 151,994 control chromosomes in the GnomAD database, including 23,713 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 0.53 (23713 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.394
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.866 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: 0.529 AC: 80299 AN: 151876 Hom.: 23658 Cov.: 32

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.529 AC: 80420 AN: 151994 Hom.: 23713 Cov.: 32 AF XY: 0.535 AC XY: 39746 AN XY: 74278

African (AFR) AF: 0.763 AC: 31636 AN: 41456

American (AMR) AF: 0.560 AC: 8554 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1531 AN: 3466

East Asian (EAS) AF: 0.887 AC: 4580 AN: 5162

South Asian (SAS) AF: 0.591 AC: 2846 AN: 4818

European-Finnish (FIN) AF: 0.399 AC: 4204 AN: 10538

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.375 AC: 25500 AN: 67954

Other (OTH) AF: 0.530 AC: 1121 AN: 2114

Alfa AF: 0.283 Hom.: 633

Bravo AF: 0.553

Asia WGS AF: 0.759 AC: 2639 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	0.91
DANN	Benign	0.41
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs6569686; hg19: chr6-130829694;