rs888539

Variant names:

• chr7-131769449-G-A
• rs888539

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.143 in 152,170 control chromosomes in the GnomAD database, including 1,616 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 0.14 (1616 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.77
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21708 AN: 152050 Hom.: 1617 Cov.: 33

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0894

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.143 AC: 21722 AN: 152170 Hom.: 1616 Cov.: 33 AF XY: 0.143 AC XY: 10653 AN XY: 74384

African (AFR) AF: 0.156 AC: 6469 AN: 41522

American (AMR) AF: 0.102 AC: 1560 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0894 AC: 310 AN: 3468

East Asian (EAS) AF: 0.100 AC: 519 AN: 5174

South Asian (SAS) AF: 0.108 AC: 520 AN: 4812

European-Finnish (FIN) AF: 0.192 AC: 2033 AN: 10582

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9951 AN: 68010

Other (OTH) AF: 0.123 AC: 261 AN: 2114

Alfa AF: 0.140 Hom.: 5768

Bravo AF: 0.135

Asia WGS AF: 0.136 AC: 476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	20
DANN	Benign	0.78
PhyloP100		2.8

Splicing

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

Other links and lift over

dbSNP: rs888539; hg19: chr7-131454208;