rs559156

Variant names:

• chr6-165250303-C-A
• rs559156

Your query was ambiguous. Multiple possible variants found:

• chr6-165250303-C-A
• chr6-165250303-C-G
• chr6-165250303-C-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 0.185 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.260 AC: 10771 AN: 41484

American (AMR) AF: 0.139 AC: 2130 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1026 AN: 3472

East Asian (EAS) AF: 0.0541 AC: 280 AN: 5180

South Asian (SAS) AF: 0.138 AC: 663 AN: 4814

European-Finnish (FIN) AF: 0.107 AC: 1137 AN: 10598

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11598 AN: 67998

Other (OTH) AF: 0.200 AC: 422 AN: 2114

Alfa AF: 0.177 Hom.: 7489

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
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs559156; hg19: chr6-165663792;