rs1551808

Variant names:

• chr6-153939812-A-G
• rs1551808

Your query was ambiguous. Multiple possible variants found:

• chr6-153939812-A-G
• chr6-153939812-A-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 0.289 in 152,104 control chromosomes in the GnomAD database, including 6,597 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 0.29 (6597 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.817
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.42 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: 0.289 AC: 43878 AN: 151986 Hom.: 6590 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.289 AC: 43894 AN: 152104 Hom.: 6597 Cov.: 32 AF XY: 0.294 AC XY: 21853 AN XY: 74356

African (AFR) AF: 0.247 AC: 10256 AN: 41480

American (AMR) AF: 0.429 AC: 6553 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 997 AN: 3470

East Asian (EAS) AF: 0.388 AC: 2007 AN: 5170

South Asian (SAS) AF: 0.412 AC: 1985 AN: 4816

European-Finnish (FIN) AF: 0.278 AC: 2936 AN: 10574

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18089 AN: 67990

Other (OTH) AF: 0.305 AC: 644 AN: 2114

Alfa AF: 0.285 Hom.: 3076

Bravo AF: 0.293

Asia WGS AF: 0.411 AC: 1430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	12
DANN	Benign	0.56
PhyloP100		0.82

Splicing

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

Other links and lift over

dbSNP: rs1551808; hg19: chr6-154260947;