rs888539

Variant names:

• chr7-131769449-G-A
• rs888539

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.143 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

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.0894

Gnomad4 EAS AF: 0.100

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.123

Alfa AF: 0.139 Hom.: 2460

Bravo AF: 0.135

Asia WGS AF: 0.136 AC: 476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs888539; hg19: chr7-131454208;