rs1555089

Variant names:

• chr6-24648178-G-A
• rs1555089

Your query was ambiguous. Multiple possible variants found:

• chr6-24648178-G-A
• chr6-24648178-G-C
• chr6-24648178-G-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 0.703 in 152,100 control chromosomes in the GnomAD database, including 38,181 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 0.70 (38181 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.306
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.703 AC: 106894 AN: 151982 Hom.: 38153 Cov.: 32

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.875

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.707

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

GnomAD4 genome AF: 0.703 AC: 106973 AN: 152100 Hom.: 38181 Cov.: 32 AF XY: 0.700 AC XY: 52025 AN XY: 74330

African (AFR) AF: 0.796 AC: 33035 AN: 41510

American (AMR) AF: 0.767 AC: 11724 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2162 AN: 3470

East Asian (EAS) AF: 0.875 AC: 4519 AN: 5166

South Asian (SAS) AF: 0.696 AC: 3356 AN: 4824

European-Finnish (FIN) AF: 0.539 AC: 5694 AN: 10556

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.648 AC: 44021 AN: 67968

Other (OTH) AF: 0.712 AC: 1506 AN: 2116

Alfa AF: 0.684 Hom.: 13162

Bravo AF: 0.725

Asia WGS AF: 0.793 AC: 2756 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.057
DANN	Benign	0.21
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs1555089; hg19: chr6-24648406;