rs559156

chr6-165250303-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.185 in 152,146 control chromosomes in the GnomAD database, including 2,871 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 0.19 (2871 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.572

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28199 AN: 152028 Hom.: 2869 Cov.: 33

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.0543

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.185 AC: 28222 AN: 152146 Hom.: 2871 Cov.: 33 AF XY: 0.180 AC XY: 13414 AN XY: 74372

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.0541

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.200

Alfa AF: 0.176 Hom.: 3300

Bravo AF: 0.191

Asia WGS AF: 0.114 AC: 397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.19
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs559156; hg19: chr6-165663792;