rs6887595

chr5-95632404-C-G

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 0.116 in 152,176 control chromosomes in the GnomAD database, including 1,624 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 0.12 (1624 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.262

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17568 AN: 152058 Hom.: 1607 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.0839

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0805

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.116 AC: 17620 AN: 152176 Hom.: 1624 Cov.: 32 AF XY: 0.122 AC XY: 9057 AN XY: 74386

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.0839

Gnomad4 EAS AF: 0.559

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.0806

Gnomad4 OTH AF: 0.120

Alfa AF: 0.0953 Hom.: 109

Bravo AF: 0.119

Asia WGS AF: 0.309 AC: 1077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.7
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6887595; hg19: chr5-94968108;