rs288945

Variant names:

• chr6-156565700-G-A
• rs288945

Your query was ambiguous. Multiple possible variants found:

• chr6-156565700-G-A
• chr6-156565700-G-T

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 0.158 in 152,118 control chromosomes in the GnomAD database, including 2,008 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 0.16 (2008 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.833

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.185 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: 0.158 AC: 23985 AN: 152000 Hom.: 2003 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0914

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.158 AC: 24011 AN: 152118 Hom.: 2008 Cov.: 32 AF XY: 0.159 AC XY: 11807 AN XY: 74368

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.0916

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.228

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.146

Alfa AF: 0.176 Hom.: 608

Bravo AF: 0.149

Asia WGS AF: 0.161 AC: 557 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.31
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs288945; hg19: chr6-156886834;