5-69445515-A-T

Variant names:

• chr5-69445515-A-T
• rs299078

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 0.529 in 151,920 control chromosomes in the GnomAD database, including 21,311 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 0.53 (21311 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.00
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.58 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: 0.529 AC: 80281 AN: 151800 Hom.: 21297 Cov.: 31

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.529 AC: 80340 AN: 151920 Hom.: 21311 Cov.: 31 AF XY: 0.535 AC XY: 39751 AN XY: 74252

African (AFR) AF: 0.506 AC: 20944 AN: 41382

American (AMR) AF: 0.590 AC: 8995 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 2050 AN: 3472

East Asian (EAS) AF: 0.558 AC: 2886 AN: 5174

South Asian (SAS) AF: 0.582 AC: 2806 AN: 4820

European-Finnish (FIN) AF: 0.595 AC: 6277 AN: 10542

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.509 AC: 34591 AN: 67972

Other (OTH) AF: 0.525 AC: 1109 AN: 2112

Alfa AF: 0.524 Hom.: 2620

Bravo AF: 0.525

Asia WGS AF: 0.578 AC: 1999 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.0030
DANN	Benign	0.20
PhyloP100		-4.0

Splicing

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

Other links and lift over

dbSNP: rs299078; hg19: chr5-68741342; COSMIC: COSV57780053;