5-86263315-T-C

Variant names:

• chr5-86263315-T-C
• rs6888626

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 0.972 in 152,254 control chromosomes in the GnomAD database, including 72,228 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 0.97 (72228 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.708
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.992 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: 0.972 AC: 147914 AN: 152136 Hom.: 72174 Cov.: 32

Gnomad AFR AF: 0.996

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.845

Gnomad ASJ AF: 0.996

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.963

Gnomad FIN AF: 0.939

Gnomad MID AF: 1.00

Gnomad NFE AF: 0.999

Gnomad OTH AF: 0.967

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

GnomAD4 genome AF: 0.972 AC: 148023 AN: 152254 Hom.: 72228 Cov.: 32 AF XY: 0.966 AC XY: 71916 AN XY: 74412

African (AFR) AF: 0.996 AC: 41372 AN: 41550

American (AMR) AF: 0.844 AC: 12898 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.996 AC: 3458 AN: 3472

East Asian (EAS) AF: 0.871 AC: 4495 AN: 5162

South Asian (SAS) AF: 0.963 AC: 4649 AN: 4826

European-Finnish (FIN) AF: 0.939 AC: 9965 AN: 10610

Middle Eastern (MID) AF: 1.00 AC: 294 AN: 294

European-Non Finnish (NFE) AF: 0.999 AC: 67935 AN: 68032

Other (OTH) AF: 0.967 AC: 2045 AN: 2114

Alfa AF: 0.992 Hom.: 9653

Bravo AF: 0.964

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.96
DANN	Benign	0.26
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs6888626; hg19: chr5-85559133;